{"_id":"58ffd7c5cd60430f006f64a3","user":"5613e4f8fdd08f2b00437620","category":{"_id":"5771811e27a5c20e00030dcd","version":"55faf11ba62ba1170021a9aa","__v":0,"project":"55faf11ba62ba1170021a9a7","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-27T19:40:14.237Z","from_sync":false,"order":7,"slug":"public-projects","title":"PUBLIC PROJECTS"},"parentDoc":null,"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"__v":0,"githubsync":"","project":"55faf11ba62ba1170021a9a7","updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-04-25T23:12:05.582Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":5,"body":"##Overview\n\n[The Cancer Imaging Archive (TCIA)](http://www.cancerimagingarchive.net/) contains radiological imaging data from [The Cancer Genome Atlas (TCGA)](http://cancergenome.nih.gov/) and is part of an effort to build a research community focused on connecting cancer phenotypes to genotypes by providing clinical images matched to subjects. \n\nTCIA includes radiological images which represent 21 types of cancer detailed in TCGA. All images are accessible for public use. These images are de-identified to ensure that images are free of protected health information (PHI), and are stored in a standard [DICOM](https://en.wikipedia.org/wiki/DICOM) format.\n\nLearn more about [TCIA data](doc:tcia-data) available in the public project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Access the TCIA public project\n\n1. Click on Public projects from the top navigation bar.\n2. Select The Cancer Imaging Archive (TCIA).\nYou'll be taken to the main dashboard of the TCIA public project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Use the TCIA public project\n\nAll CGC users automatically have copy permissions for this project. This means that while you cannot upload data or tools to the project, you can copy the available data to your own projects on the CGC to execute analyses.\n\nYou have the options to:\n* **[Copy the entire project](#section-copy-the-entire-project)** - Start from the copied project and add apps to execute analyses on TCIA data.\n* **[Select and copy a subset of the data to your own project](#section-use-a-subset-of-the-data)** - Use the selected data within your own analyses in your project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Copy the entire project\n\n1. Access the TCIA public project by selecting **The Cancer Imaging Archive (TCIA)** from **Public projects** in the top navigation bar.\n2. Click **Copy this project**, next to the project's title, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/b4a8e7c-Screen_Shot_2017-04-27_at_2.50.31_PM.png\",\n        \"Screen Shot 2017-04-27 at 2.50.31 PM.png\",\n        1431,\n        622,\n        \"#f9f9f8\"\n      ]\n    }\n  ]\n}\n[/block]\n3. In the pop-up window, optionally name your copy of the project and select a billing group.\n4. Once you've customized the details, click **Copy to copy the entire project**.\n\nYou'll be redirected to the dashboard of your cloned project. Add apps to conduct analyses on the data in your project.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Use a subset of the data\n\nInstead of cloning the entire project, you can choose to select and copy a subset of the data.\n\n1. Access the TCIA public project by selecting The Cancer Imaging Archive (TCIA) from Public projects in the top navigation bar.\n2. Click the Files tab in the upper righthand corner. This will take you to the Files page for the TCIA project, as shown below.\n3. Filter or search for the desired files. You can filter by:\n\n* Keywords - You can use the search bar at the top of the page to find files by entering the file name or notes associated with a file.\n* Metadata fields - Next to the search bar, you will see drop-down menus for the metadata fields.\n\n<div style=\"margin-left:3em\">\nSelecting a particular metadata value from one of these menus displays only files that match the value. You can add additional drop-down menus to filter by other metadata fields by clicking the + icon.\n\nFor instance, filter by the metadata field Investigation and select files with **TCGA-GBM** for images from patients with **Glioblastoma Multiforme**. Or, to find images derived from **Magnetic Resonance Imaging**, filter by the metadata field **Modality** and select files with **MR**.</div>\n\n4. Choose specific files by checking the corresponding box by each file name.\n5. Select as many files as you desire and click **Copy to**.\n6. Select your target project from the drop-down menu.\n\nNow, you can start using the TCIA files you've added to your personal project in your own analysis.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"the-cancer-imaging-archive-tcia-project","type":"basic","title":"The Cancer Imaging Archive (TCIA) project"}

The Cancer Imaging Archive (TCIA) project


##Overview [The Cancer Imaging Archive (TCIA)](http://www.cancerimagingarchive.net/) contains radiological imaging data from [The Cancer Genome Atlas (TCGA)](http://cancergenome.nih.gov/) and is part of an effort to build a research community focused on connecting cancer phenotypes to genotypes by providing clinical images matched to subjects. TCIA includes radiological images which represent 21 types of cancer detailed in TCGA. All images are accessible for public use. These images are de-identified to ensure that images are free of protected health information (PHI), and are stored in a standard [DICOM](https://en.wikipedia.org/wiki/DICOM) format. Learn more about [TCIA data](doc:tcia-data) available in the public project. <div align="right"><a href="#top">top</a></div> ##Access the TCIA public project 1. Click on Public projects from the top navigation bar. 2. Select The Cancer Imaging Archive (TCIA). You'll be taken to the main dashboard of the TCIA public project. <div align="right"><a href="#top">top</a></div> ##Use the TCIA public project All CGC users automatically have copy permissions for this project. This means that while you cannot upload data or tools to the project, you can copy the available data to your own projects on the CGC to execute analyses. You have the options to: * **[Copy the entire project](#section-copy-the-entire-project)** - Start from the copied project and add apps to execute analyses on TCIA data. * **[Select and copy a subset of the data to your own project](#section-use-a-subset-of-the-data)** - Use the selected data within your own analyses in your project. <div align="right"><a href="#top">top</a></div> ###Copy the entire project 1. Access the TCIA public project by selecting **The Cancer Imaging Archive (TCIA)** from **Public projects** in the top navigation bar. 2. Click **Copy this project**, next to the project's title, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/b4a8e7c-Screen_Shot_2017-04-27_at_2.50.31_PM.png", "Screen Shot 2017-04-27 at 2.50.31 PM.png", 1431, 622, "#f9f9f8" ] } ] } [/block] 3. In the pop-up window, optionally name your copy of the project and select a billing group. 4. Once you've customized the details, click **Copy to copy the entire project**. You'll be redirected to the dashboard of your cloned project. Add apps to conduct analyses on the data in your project. <div align="right"><a href="#top">top</a></div> ###Use a subset of the data Instead of cloning the entire project, you can choose to select and copy a subset of the data. 1. Access the TCIA public project by selecting The Cancer Imaging Archive (TCIA) from Public projects in the top navigation bar. 2. Click the Files tab in the upper righthand corner. This will take you to the Files page for the TCIA project, as shown below. 3. Filter or search for the desired files. You can filter by: * Keywords - You can use the search bar at the top of the page to find files by entering the file name or notes associated with a file. * Metadata fields - Next to the search bar, you will see drop-down menus for the metadata fields. <div style="margin-left:3em"> Selecting a particular metadata value from one of these menus displays only files that match the value. You can add additional drop-down menus to filter by other metadata fields by clicking the + icon. For instance, filter by the metadata field Investigation and select files with **TCGA-GBM** for images from patients with **Glioblastoma Multiforme**. Or, to find images derived from **Magnetic Resonance Imaging**, filter by the metadata field **Modality** and select files with **MR**.</div> 4. Choose specific files by checking the corresponding box by each file name. 5. Select as many files as you desire and click **Copy to**. 6. Select your target project from the drop-down menu. Now, you can start using the TCIA files you've added to your personal project in your own analysis. <div align="right"><a href="#top">top</a></div>