{"id":42613,"date":"2023-11-20T02:40:19","date_gmt":"2023-11-20T08:40:19","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/collection\/ispy2\/"},"modified":"2024-09-27T11:46:42","modified_gmt":"2024-09-27T16:46:42","slug":"ispy2","status":"publish","type":"tcia_collection","link":"https:\/\/stage.cancerimagingarchive.net\/collection\/ispy2\/","title":{"rendered":"ISPY2"},"featured_media":7199,"template":"","class_list":["post-42613","tcia_collection","type-tcia_collection","status-publish","has-post-thumbnail"],"cancer_types":["Breast Cancer"],"citations":[42599,42601,42603,9225],"collection_doi":"10.7937\/TCIA.D8Z0-9T85","collection_download_info":"","collection_downloads":[42605,42607,42609,42611,48297,48299,48301],"versions":false,"additional_resources":"The NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.\r\n<ul>\r\n \t<li><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=ispy2\">Imaging Data Commons (IDC)<\/a> (Imaging Data)<\/li>\r\n<\/ul>\r\nThe following external resources are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.\r\n<ul>\r\n \t<li><a href=\"https:\/\/clinicaltrials.gov\/\">ClinicalTrials.gov<\/a> entry about the Trial <a href=\"https:\/\/clinicaltrials.gov\/study\/NCT01042379\">NCT01042379 \"I-SPY TRIAL: Neoadjuvant and Personalized Adaptive Novel Agents to Treat Breast Cancer (I-SPY), (Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging And moLecular Analysis 2)\" <\/a><\/li>\r\n<\/ul>","cancer_locations":["Breast"],"collection_page_accessibility":"Public","publications_related":"","version_change_log_archived":"<h3>Note:<\/h3><p>On 7\/8\/2022 the data submitter signed off on using the <a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY 4.0<\/a> instead of the <a href=\"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/\">CC BY-NC 4.0<\/a>.<\/p><h3>Version 1 (Current): Updated 2022\/05\/02<\/h3><table><colgroup><col \/><col \/><col \/><\/colgroup><tbody><tr><th>Data Type<\/th><th>Download all or Query\/Filter<\/th><th>License<\/th><\/tr><tr><td><p>Images (DICOM, 1.6 TB)<\/p><p>719 patients<\/p><\/td><td><div><p><br \/><a href=\"\/wp-content\/uploads\/ISPY2-719-patients-only-manifest-Jan-2022.tcia\" download=\"ISPY2-719-patients-only-manifest-Jan-2022.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0 <a href=\"https:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?MinNumberOfStudiesCriteria=1&amp;CollectionCriteria=ISPY2\"><button><i><\/i> Search<\/button><\/a>\u00a0<\/p><p><strong>Note:<\/strong>\u00a0When DICOM data are downloaded with the NBIA Data Retriever, the app uses \"Series Description\" values to construct descriptive directory names. In some series for this Collection, characters that are not allowed in directory names are present. So the workaround is to select the \u201cClassic Directory Name\u201d option, which is located above \u201cSelect Directory For Downloaded Files.\u201d\u00a0<\/p><p>(Download requires\u00a0the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/\">CC BY-NC 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td><p>Images (DICOM, 2.4 TB)<\/p><p>I-SPY2 Imaging Cohort 1 dataset, 985 patients<\/p><\/td><td><div><p><a href=\"\/wp-content\/uploads\/ISPY2-Cohort1-inclu-ACRIN6698-full-manifest.tcia\" download=\"ISPY2-Cohort1-inclu-ACRIN6698-full-manifest.tcia\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/\">CC BY-NC 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td><p>Clinical data (CSV)<\/p><p>I-SPY2 Imaging Cohort 1 dataset, 985 patients<\/p><\/td><td><div><p><br \/><a href=\"\/wp-content\/uploads\/ISPY2-Imaging-Cohort-1-Clinical-Data.xlsx\" download=\"ISPY2-Imaging-Cohort-1-Clinical-Data.xlsx\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/\">CC BY-NC 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td><p>Multi-feature MRI NACT Data (.xlsx)<\/p><p>\u201c<a href=\"https:\/\/doi.org\/10.1038\/s41523-020-00203-7\">Predicting breast cancer response to neoadjuvant treatment using multi-feature MRI: results from the I-SPY 2 TRIAL<\/a>\u201d cohort, 384 patients<\/p><\/td><td><div><p><a href=\"\/wp-content\/uploads\/Multi-feature-MRI-NACT-Data.xlsx\" download=\"Multi-feature-MRI-NACT-Data.xlsx\"><button><i><\/i> Download<\/button><\/a>\u00a0<\/p><\/div><\/td><td><div><p><a href=\"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/\">CC BY-NC 4.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table>","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 publication you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","related_analysis_results":false,"species":["Human"],"version_number":"1","collection_title":"I-SPY 2 Breast Dynamic Contrast Enhanced MRI Trial","date_updated":"2022-05-02","related_collection":false,"subjects":"719","analysis_results":"","collection_short_title":"ISPY2","data_types":["MR","SEG"],"version_change_log":"","collection_browse_title":"I-SPY2 Trial","detailed_description":"<h3>MRI Studies<\/h3>\r\n<h4>Trial time points for MRI studies<\/h4>\r\nMRI studies were performed at up to four time points in the course of NAC:\r\n<ol>\r\n \t<li>Pre-treatment (T0, optional test\/retest visit)\r\nPrior to randomization patients received an MRI study including T2<sub>weighted<\/sub>, DWI, and dynamic contrast-enhanced (DCE) acquisitions.<\/li>\r\n<\/ol>\r\nFor patients randomized onto a treatment or control arm of I\u2011SPY\u00a02 subsequent MRI studies with the same required acquisitions were performed:\r\n<ol>\r\n \t<li>Early-treatment (T1, optional test\/retest visit)\r\nAfter 3 weeks of regimen 1 treatment (Paclitaxel with or without an experimental agent).<\/li>\r\n \t<li>Mid-treatment (T2)\r\nBetween Paclitaxel and Anthracycline (AC) treatment regimens<\/li>\r\n \t<li>Post-treatment (T3)\r\nFollowing 4 cycles AC and prior to surgery.<\/li>\r\n<\/ol>\r\n<strong><a href=\"\/wp-content\/uploads\/I-SPY2_schema_TCIA.jpg\" rel=\"prettyPhoto noopener\"><img class=\"cm-inline-img-css alignright wp-image-625 size-medium\" src=\"\/wp-content\/uploads\/I-SPY2_schema_TCIA.jpg\" \/><\/a><\/strong>\r\n\r\nFigure 1. I-SPY 2 study schema.\r\n<h4>Imaging protocol and included original image series<\/h4>\r\nMR imaging was performed on a 1.5 or 3.0 Tesla scanner using a dedicated breast radiofrequency coil. All studies for a given patient were required to be performed on the same scanner configuration (model, field strength and breast coil model). Subjects were imaged in the prone position. The image acquisition protocol included a localization scan and two acquisitions:\r\n<ol>\r\n \t<li>T2<sub>weighted<\/sub> sequence<\/li>\r\n \t<li>T1<sub>weighted<\/sub> DCE (80sec &lt; phase duration &lt; 100sec with at least 8 minutes continuous post-injection acquisition)<\/li>\r\n<\/ol>\r\nThe DWI acquisitions (b=0, 100, 600, 800 s\/mm<sup>2<\/sup>\u00a0OR b=0, 800) were also acquired but\u00a0are undergoing quality review and are not included in the collection at this time.\r\n\r\nProtocol limits on scan parameters for these required acquisitions are given in an accompanying document\r\n\r\nAll required imaging was performed axially with full bilaterally coverage. For the TCIA collection all original images from the two acquisitions are included. Derived images submitted with the study including reformats, CAD software outputs and MIP images are not part of the collection. For the T2<sub>weighted<\/sub>\u00a0acquisitions multiple series are included if they were generated as part of the standard reconstruction process on the scanner. For example, acquisitions utilizing Dixon techniques to create separate fat and water images will have multiple T2<sub>weighted<\/sub> series in the collection.\r\n<h4>Derived object series:<\/h4>\r\nDerived objects from the DCE acquisitions are included for the convenience of the user. Some of these are not strictly DICOM compliant and may not be readable by all DICOM software packages. Parametric maps and segmentations are believed to be identical to those utilized in the primary analyses of the I-SPY 2 Trial, but in some cases modifications may have occurred in subsequent processing.\r\n<h5>DCE \u201cPackage\u201d for each study<\/h5>\r\n<ol>\r\n \t<li>Single-breast ipsilateral cropped DCE images\r\n<ol>\r\n \t<li>As this was done primarily for computational efficiency, low matrix-sized images (&lt;384 voxels per row) were stored and processed without cropping<\/li>\r\n \t<li>All maps and segmentations are based on these cropped images<\/li>\r\n<\/ol>\r\n<\/li>\r\n \t<li>Enhancement maps\r\n<ol>\r\n \t<li>PE<sub>early<\/sub>: Percent enhancement at effective post-contrast time 120-150 sec<\/li>\r\n \t<li>PE<sub>late<\/sub>: Percent enhancement at effective post-contrast time ~450 sec<\/li>\r\n \t<li>SER: Signal enhancement ratio\u00a0\u00a0\u00a0 SER =\u00a0 PE<sub>early<\/sub> \/ PE<sub>late<\/sub>\r\nNote: SER values were scaled by 1000 to allow integer storage. DICOM software utilizing the rescale slope and intercept fields [ DICOM fields (0028, 1052-1054)] should return the original SER values in the range from 0.0 \u2013 3.0.<\/li>\r\n \t<li>All maps are stored as DICOM MRI objects<\/li>\r\n<\/ol>\r\n<\/li>\r\n \t<li>Functional Tumor Volume (FTV) analysis mask\r\n<ol>\r\n \t<li>Image storing FTV masking processes on a pixel-by-pixel basis. The mask encodes:\r\n<ol>\r\n \t<li>Pre-contrast background thresholding<\/li>\r\n \t<li>Minimum PE thresholding (70% nom.)<\/li>\r\n \t<li>Manually defined rectangular volume of interest (VOI) for enhancing tumor analysis<\/li>\r\n \t<li>Manually defined \u201cOMIT\u201d regions used to exclude non-tumor enhancing regions that encroached on the rectangular VOI<\/li>\r\n<\/ol>\r\n<\/li>\r\n \t<li>Stored as DICOM SEG object in a separate series (see Table 1)<\/li>\r\n \t<li>Download\u00a0<a href=\"\/wp-content\/uploads\/Analysis-mask-files-description.v20211020.docx\" download=\"Analysis-mask-files-description.v20211020.docx\">Analysis mask files description<\/a> for further information:<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\nThese DCE derived series can be identified either by Series Description (0008,103e) or by Series Number (0020,0011). See Table 1 for series identification details.\r\n\r\nTable 1. Series identification for derived DCE objects\r\n<table><colgroup> <col \/> <col \/> <col \/><\/colgroup>\r\n<tbody>\r\n<tr>\r\n<td data-highlight-colour=\"green\">\r\n<p title=\"\"><strong>Data type<\/strong><\/p>\r\n<\/td>\r\n<td data-highlight-colour=\"green\">\r\n<p title=\"\"><strong>Series number<\/strong><\/p>\r\n<\/td>\r\n<td data-highlight-colour=\"green\">\r\n<p title=\"\"><strong>Series Description Match<\/strong><\/p>\r\n<\/td>\r\n<\/tr>\r\n<tr>\r\n<th>DCE \u00a0 \u00a0 root directory #<\/th>\r\n<th colspan=\"2\">Siemens, GEMS:\u00a0 &lt;root&gt; = 1<sup>st<\/sup> original DCE series number\r\n\r\nPhilips:\u00a0 &lt;root&gt; = Original DCE series number \/ 100<\/th>\r\n<\/tr>\r\n<tr>\r\n<td>SER Map<\/td>\r\n<td>&lt;root&gt;1000<\/td>\r\n<td>ISPY2: VOLSER: uni-lateral cropped: SER <sup>2<\/sup><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>PE phase &lt;n&gt; Map<\/td>\r\n<td>&lt;root&gt;100&lt;n&gt;<\/td>\r\n<td>ISPY2: VOLSER: uni-lateral cropped: PE&lt;n&gt; <sup>2<\/sup><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Ipsilateral cropped Original<\/td>\r\n<td>&lt;root&gt;1800<\/td>\r\n<td>ISPY2: VOLSER: uni-lateral cropped: original DCE <sup>2<\/sup><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>FTV Analysis Mask<sup>1<\/sup><\/td>\r\n<td>&lt;root&gt;1900<\/td>\r\n<td>ISPY2: VOLSER: uni-lateral cropped: Analysis Mask <sup>2<\/sup><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<ol>\r\n \t<li>FTV Analysis Masks are bit-encoded segmentations encoding all masking steps in the I\u2011SPY\u00a02 primary FTV analysis. See document <a href=\"\/wp-content\/uploads\/Analysis-mask-files-description.v20211020.docx\" download=\"Analysis-mask-files-description.v20211020.docx\">Analysis mask files description<\/a>\u00a0for a full description of these objects.<\/li>\r\n \t<li>DCE images with less than 384 voxels\/row were not cropped for the FTV analysis. For these studies the derived DCE objects are all full bilateral images.<\/li>\r\n<\/ol>\r\n<h4>DICOM Dictionary for UCSF Private Attributes in Derived Objects:<\/h4>\r\nCalculation parameters and DCE volume analysis results are included in private attributes in some of the derived objects. <a href=\"\/wp-content\/uploads\/ACRIN-6698-ISPY2-Shared-Private-Tag-Data-Dictionary_20210520.xlsx\" download=\"ACRIN-6698-ISPY2-Shared-Private-Tag-Data-Dictionary_20210520.xlsx\">ACRIN 6698 ISPY2 Shared Private Tag Data Dictionary <\/a>and\u00a0<a href=\"\/wp-content\/uploads\/ACRIN-6698-ISPY2-DWI-and-DCE-MRI-Data-Descriptions_20210520.pdf\" download=\"ACRIN-6698-ISPY2-DWI-and-DCE-MRI-Data-Descriptions_20210520.pdf\">ACRIN 6698 ISPY2 DWI and DCE MRI Data Descriptions<\/a>\u00a0files are provided for download for researchers wishing to use these parameters and\/or results from the primary analyses. Note: the DCE functional tumor volume (FTV) results stored in the SER derived objects are NOT identical to those used in the I\u2011SPY\u00a02 study due to differences in implementations on different platforms (UCSF in-house software vs. Hologic Inc. AEGIS system). While the differences are generally small and the AEGIS system was validated against the UCSF results in the prior I\u2011SPY\u00a01 TRIAL, identical results cannot be guaranteed.","supporting_data":["Clinical","Image Analyses"],"collection_featured_image":{"ID":"7199","post_author":"29","post_date":"2023-09-13 09:34:40","post_date_gmt":"2023-09-13 14:34:40","post_content":"","post_title":"I-SPY2_schema_TCIA","post_excerpt":"","post_status":"inherit","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"i-spy2_schema_tcia","to_ping":"","pinged":"","post_modified":"2023-11-20 02:40:20","post_modified_gmt":"2023-11-20 08:40:20","post_content_filtered":"","post_parent":"42613","guid":"https:\/\/stage.cancerimagingarchive.net\/wp-content\/uploads\/I-SPY2_schema_TCIA.jpg","menu_order":"0","post_type":"attachment","post_mime_type":"image\/jpeg","comment_count":"0","pod_item_id":"7199"},"collection_summary":"<p>I-SPY 2 (Investigation of Serial studies to Predict Your Therapeutic Response with Imaging And moLecular analysis 2) is an ongoing, multi-center trial (<a href=\"https:\/\/clinicaltrials.gov\/ct2\/show\/NCT01042379\">NCT01042379<\/a>) designed to quickly evaluate the efficacy of new agents for breast cancer in neoadjuvant chemotherapy (NAC) setting. Women aged \u226518 years diagnosed with locally advanced breast cancer (tumor size \u22652.5 cm) without distant metastasis are eligible to enroll in the trial. Patients with breast cancer at high-risk for recurrence are adaptively-randomized to either control arm (standard NAC) or one of several concurrent experimental drug arms. I-SPY 2 utilizes change in tumor volume by DCE-MRI at serial time-points during NAC to adjust the randomization schema as the trial proceeds, preferentially assigning patients to receive agents showing an increasing likelihood of efficacy against their breast cancer subtype. I-SPY 2 opened in Spring 2010 and is ongoing.<\/p><p>This collection includes DCE MRI data (original acquired images and derived parametric maps) for I-SPY 2 patients adaptively randomized between 2010 and 2016, along with histopathologic outcome data. Breast MRI data in this collection was acquired prospectively at over 22 clinical centers using a standardized image acquisition protocol. Patients underwent 4 MRI exams before and during NAC and over 95% of the DCE imaging data met acceptance criteria for analysis of functional tumor volume (FTV), a demonstrated quantitative imaging marker of breast cancer response to NAC. This is a comprehensive, highly curated imaging data set with histopathologic outcome that can be used to develop, test and compare imaging metrics and prediction models for breast cancer response to treatment. Original but uncurated T2<sub>weighted<\/sub> MRI images are also included for most studies.<\/p><p>719 patients are included in this collection. In combination with 266 patients from the <a href=\"\/collection\/acrin-6698\/\">ACRIN 6698\/I-SPY2 Breast DWI<\/a> Collection these 985 patients comprise \"I-SPY2 Imaging Cohort 1\", the 1st subgroup of publicly released imaging data from the I-SPY 2 TRIAL. All subjects in the I-SPY2 Imaging Cohort 1 were enrolled in I-SPY 2 from 2010 to 2016 and randomized to one of nine completed experimental drug arms or control arm. In order to obtain the MRI data for the entire I-SPY2 Imaging Cohort 1 please download using the manifest file provided in the Data Access table below as this will include the patients from both collections. Downloading this collection alone will result in an incomplete cohort of 719 patients and any results from that patient set will not be comparable to published results from the trial.<\/p><p>In addition, a retrospective study using a 384 patient subset (median age: 49\u2009y\/o) was performed to test if prediction models combining multiple MRI features outperform models with single features. Four features were quantitatively calculated in each MRI exam: functional tumor volume, longest diameter, sphericity, and contralateral background parenchymal enhancement. Logistic regression analysis was used to study the relationship between MRI variables and pathologic complete response (pCR). Predictive performance was estimated using the area under the receiver operating characteristic curve (AUC). The cohort was stratified by hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status (positive or negative). Results showed analysis with combined features achieved higher AUCs than analysis with any feature alone.\u00a0 These results are further described in the associated <a href=\"https:\/\/doi.org\/10.1038\/s41523-020-00203-7\"> publication <\/a>and in the multi-feature MRI spreadsheet included with this Collection.<\/p><h3>I-SPY2 Imaging Biomarker Group<\/h3><p>We are establishing the I-SPY 2 \u200bImaging \u200bBiomarker \u200bSubgroup to provide a forum where imaging scientists and radiologists can explore,\u200b discuss, and strategize on the use of I-SPY 2 MRI data \u200bavailable through\u00a0TCIA. \u200bPlease access\u00a0<a href=\"https:\/\/forms.office.com\/r\/u0xzwB9kbU\">https:\/\/forms.office.com\/r\/u0xzwB9kbU<\/a> to be considered to join our bimonthly Zoom meeting invite list.<\/p>","collection_acknowledgements":"<p>The I-SPY2 Breast MRI Collection is supported by NIH grants U01 CA225427, R01 CA132870 and P01 CA210961. The I-SPY 2 TRIAL is supported by the Quantum Leap Healthcare Collaborative. The authors gratefully acknowledge and thank the patients who have volunteered to participate in the I-SPY2 TRIAL, as well as the extensive network of investigators, patient advocates and study coordinators. We especially thank the site radiology teams that have contributed substantially to the value of this archive.<\/p>","collection_funding":"","hide_from_browse_table":"0","program":["NCI Trials"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42613","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_collection"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42613\/revisions"}],"predecessor-version":[{"id":47515,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/collections\/42613\/revisions\/47515"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media\/7199"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=42613"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}