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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>Home on Yarra Framework</title>
<link>http://yarra-framework.org/</link>
<description>Recent content in Home on Yarra Framework</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Wed, 30 May 2018 00:00:00 +0000</lastBuildDate><atom:link href="http://yarra-framework.org/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>Basic GRASP (Matlab)</title>
<link>http://yarra-framework.org/modules_user/grasp-basic/</link>
<pubDate>Mon, 15 Jul 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_user/grasp-basic/</guid>
<description>Purpose This module provides a stable Matlab implementation of the GRASP DCE-MRI reconstruction technique. It requires Matlab R2016a or newer. If the Parallel Computing Toolbox has been installed, the reconstruction will be parallelized across slices depending on the available CPU cores. By default, all available cores will be used for the calculation.
When using the module, please cite the following publication:
Feng L, Grimm R, Block KT, Chandarana H, Kim S, Xu J, Axel L, Sodickson DK, Otazo R.</description>
</item>
<item>
<title>Client Tools</title>
<link>http://yarra-framework.org/addons/clienttools/</link>
<pubDate>Wed, 03 Jul 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/addons/clienttools/</guid>
<description>&nbsp;IntroductionThe Yarra Client Tools (YCT) are several small command-line tools for Windows that can be helpful when working with Siemens raw-data files (aka Twix files). They are distributed in a separate package because they are targeted at advanced users. It is recommended to extract the package into the installation folder of the Yarra Client package because the tools require runtime libraries that are contained in the Yarra Client package.</description>
</item>
<item>
<title>Core Modules</title>
<link>http://yarra-framework.org/modules/core/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules/core/</guid>
<description>&nbsp;Included Core ModulesThe following &ldquo;core&rdquo; modules are included in the YarraServer installation package. The binaries are located in the folder yarra/modules. They can be referenced using the helper macro %bd. Sometimes, beta versions of updated core modules are released. It is possible to install these versions as user modules in parallel to the version that comes with the YarraServer release (in this case, the macro for calling the modules has to be replaced by %bu).</description>
</item>
<item>
<title>Installation</title>
<link>http://yarra-framework.org/clients/installation/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/clients/installation/</guid>
<description>&nbsp;Package InstallationTo install Yarra clients, download the Yarra client package form the Download Page.
Extract the archive into a folder on the host computer of the MRI system (or workstation PC for the SAC). The package can be unzipped into any directory. We recommend installing it into the folder C:\yarra.
&nbsp; Advanced User To perform this procedure on a Siemens MRI system, it is necessary to first switch to “Advanced User Mode” by selecting the item in the Start menu and entering the password.</description>
</item>
<item>
<title>Installation</title>
<link>http://yarra-framework.org/logserver/installation/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/logserver/installation/</guid>
<description>&nbsp;Installing LogServerYarra LogServer (YLS) is currently built and packaged for Ubuntu 18.04 and 20.04.
YLS is not designed to be made available to the internet. It should never be made available outside your internal network. The system uses common-sense security measures to protect patient data, but it was not designed to withstand a determined attack across the public internet.
Installation is simple. First, download the most recent yarralogserver package for your Ubuntu version here.</description>
</item>
<item>
<title>Performance-optimized GRASP (C++)</title>
<link>http://yarra-framework.org/modules_user/grasp/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_user/grasp/</guid>
<description>Purpose Performs a Compressed-Sensing-based 4D DCE-MRI reconstruction using the GRASP reconstruction technique. This module has been implemented in C++ and uses OpenMP parallelization to achieve high reconstruction speed.
Note: This module can only be downloaded after a C2P contract with Siemens has been signed. Please contact your local Siemens collaboration manager. Alternatively, the Matlab-based version of GRASP can be used.
Usage GraspR [input Twix file] [ini file] [output folder] [tmp folder] [acc #] Typical call:</description>
</item>
<item>
<title>Team</title>
<link>http://yarra-framework.org/overview/team/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/overview/team/</guid>
<description>&nbsp;Yarra Development TeamYarra has been developed by members of the Center for Advanced Imaging Innovation and Research (CAI2R) at New York University Langone Health.
&nbsp; Kai Tobias BlockTobias has been developing Yarra since 2012 after leaving his former position at Siemens Healthcare MR. He is an Associate Professor at NYU Langone Health.&nbsp; Roy WigginsRoy started working on Yarra in 2016 when he joined NYU Langone Health as Research Software Engineer.</description>
</item>
<item>
<title>Building YarraServer</title>
<link>http://yarra-framework.org/developer/build-server/</link>
<pubDate>Mon, 03 Jun 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/developer/build-server/</guid>
<description>&nbsp;Build-Instructions for YarraServer&nbsp; Setting up the Build Environment &nbsp; Download Xubuntu 16.04.06 LTS Desktop Edition and install (preferably in VM). The Desktop Edition is preferred because the Qt installation requires X11. When using VirtualBox, install the VirtualBox Guest Additions CD. Update the apt-get chache: sudo apt-get update Install build system, required tools, and required libraries: sudo apt install build-essential mercurial tortoisehg git cmakesudo apt install libboost-all-dev libssl-dev libpq-dev libssl-dev libfcgi-dev &nbsp; Installing Qt and Qt Creator &nbsp; Download the Qt offline installer and run the setup.</description>
</item>
<item>
<title>Archive Search</title>
<link>http://yarra-framework.org/addons/yas/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/addons/yas/</guid>
<description>&nbsp;IntroductionWhen collecting raw-data files from a large number of patients (e.g., through Yarra offline reconstructions or using the Yarra RDS client), it can quickly become difficult to find the data file from a certain patient or exam (as needed for performing retrospective studies). This problem is solved by Yarra Archive Search (YAS), which can be used as add-on for a YarraServer installation or completely independently from other Yarra components.</description>
</item>
<item>
<title>Configuration</title>
<link>http://yarra-framework.org/logserver/configuration/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/logserver/configuration/</guid>
<description>&nbsp;LogServer Configuration&nbsp; Initial User for Admin Interface After the installation, there won’t be any users set up in the web interface. Click the “Register” link and provide your email and set a password. LogServer will send an email with a link to verify the email address. It is recommended to only use institutional email addresses. You can skip verifying your own email address by running this command:
sudo su postgres -c &#34;psql -d yarralog -c &#39;update auth_info set email=unverified_email where id=1;&#39;&#34; After verifying your email address, you need to activate the account (this is normally done in the web interface by one of the admin accounts, but not possible for the initial user).</description>
</item>
<item>
<title>DriveTransfer</title>
<link>http://yarra-framework.org/modules_core/drivetransfer/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_core/drivetransfer/</guid>
<description>Purpose Transfers reconstructed DICOM images onto a network share (or mounted disk drive).
Usage DriveTransfer [mode file] [directory with DICOMs] [unique task name] Typical call:
[Transfer]Bin=%bd/DriveTransferArgs=%mc %td %vuid Configuration In .mode file:
[DriveTransfer]TargetPath=#Path to target location, e.g. /media/yarra_out </description>
</item>
<item>
<title>File Mover</title>
<link>http://yarra-framework.org/addons/filemover/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/addons/filemover/</guid>
<description>&nbsp;IntroductionYarra FileMover is a small helper tool that moves files regularly from a source location to an archive destination. If the file transfer fails, it sends out email notifications to specified recipients.
We are using it to move processed raw-data files from our YarraServers to a central archive location on a network share. Because the network transfer takes time, we decided to decouple the file transfer from the YarraServer process, so that the server process doesn&rsquo;t get blocked due to the transfer operation.</description>
</item>
<item>
<title>IniPatch</title>
<link>http://yarra-framework.org/modules_core/inipatch/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_core/inipatch/</guid>
<description>Purpose Creates a “patched” copy of a source ini file in the work directory with the given name. All keys specified in the mode file will be replaced by the param value passed as 4th argument, or by statically defined values written into the mode file.
Usage IniPatch [mode file] [source ini file] [target (in work dir)] [param value] Typical call:
[PreProcessing]Bin=%bd/IniPatchArgs=%mc %md/template.ini %rid/settings.ini %vparam Configuration In .mode file:</description>
</item>
<item>
<title>Installation</title>
<link>http://yarra-framework.org/server/installation/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/installation/</guid>
<description>&nbsp;Operating SystemThe currently supported operating systems for YarraServer are Ubuntu 16.04 LTS 64bit and Ubuntu 18.04 LTS 64bit, which can be downloaded here (using older Ubuntu versions is not recommended). It is possible to use both, the Server Edition as well as the Desktop Edition. It might be easier for users less familiar with Linux to use the Desktop edition because it comes with many helpful tools such as graphical editors.</description>
</item>
<item>
<title>PatchCharacterSet</title>
<link>http://yarra-framework.org/modules_user/patchcharacterset/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_user/patchcharacterset/</guid>
<description>Purpose Patches the character set of the reconstructed DICOMs and encodes the patient name in the local patient name. Necessary when using the GRASP module with certain PACS systems.
Usage PatchPatientName [input folder] [output folder] [TWIX file] Typical call:
[PostProcessing]Bin1=%bu/PatchCharacterSet/PatchPatientName.shArgs1=%pid %pod %rid/%rif Configuration The character set can be changed directly in the script PatchPatientName.sh.</description>
</item>
<item>
<title>Previous Releases</title>
<link>http://yarra-framework.org/download/archive/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/download/archive/</guid>
<description>&nbsp;Release History&nbsp; Yarra Client Package &nbsp; &nbsp;&nbsp;Version 0.65b1 &ndash; Release Date: 2024-06-11Added support for XA51, XA60, and XA61ORT: Added mechanism for tracking which cases have been submittedRDS: Added mechanism for showing notifications on scanner host&nbsp;Download Version&nbsp;&nbsp;Version 0.62 &ndash; Release Date: 2022-10-17Introduced Yarra Diagnostics toolAdded support for XA40 and XA50Updated UI designRDS: Option for alternative local buffer location&nbsp;Download Version&nbsp;&nbsp;Version 0.</description>
</item>
<item>
<title>SetDCMTags</title>
<link>http://yarra-framework.org/modules_core/setdcmtags/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_core/setdcmtags/</guid>
<description>Purpose Populates the DICOM tags of reconstructed images based on patient and scan information read from the Twix file. It also combines DICOM files into series based on the file name and sets the needed DICOM UUIDs.
Usage SetDCMTags [options] input output rawfile Parameters:
input -- Folder with DICOM files to processoutput -- Folder where modified DICOM files will be writtenrawfile -- Path and name of raw-data file Options:</description>
</item>
<item>
<title>Subtraction</title>
<link>http://yarra-framework.org/modules_user/subtraction/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_user/subtraction/</guid>
<description>Purpose Calculates subtraction images from reconstructed image series.
Usage Subtraction [input folder] [output folder] [mode file] Typical call:
[PostProcessing]Bin=%bu/Subtraction/SubtractionArgs=%pid %pod %mc Configuration In .mode file:
[Subtraction]BaselineSeries=2KeepSourceImages=trueSubtractionMode=0IncludeSeries=3:end#4ExcludeSeries= Keep source images If KeepSourceImages=false, then only the subtraction images will be sent. If KeepSourceImages=true, both the original images and subtraction images will be sent.
Subtraction mode If SubtractionMode=0, then negative values will be discarded. If SubtractionMode=1, then the absolute value of the difference is calculated.</description>
</item>
<item>
<title>Support</title>
<link>http://yarra-framework.org/overview/support/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/overview/support/</guid>
<description>&nbsp;User SupportWe are trying our best to support users of the Yarra Framework, but unfortunately our time is limited since we are a very small group. Please use our GitHub Discussions forum to send us your questions and requests. This is the most effective way for getting in touch with us and ensures that everyone from the Yarra team can answer your post. We also would like to encourage other members from the community to support users with questions on Yarra through the discussion forum.</description>
</item>
<item>
<title>User Modules</title>
<link>http://yarra-framework.org/modules/user/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules/user/</guid>
<description>&nbsp;Additional Installable ModulesAdditional modules can be installed via the module installer of the WebGUI (on the Configuration page). User modules are extracted into separate folders under the directory yarra/modules_user. The helper macro for referencing this folder is %bu. For example, when installing the Subtraction module, this binary can be called via %bu/Subtraction/Subtraction (the latter Subtraction refers to the executable name, while the former corresponds to the installation folder name).</description>
</item>
<item>
<title>Building Clients</title>
<link>http://yarra-framework.org/developer/build-client/</link>
<pubDate>Mon, 03 Jun 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/developer/build-client/</guid>
<description>&nbsp;Build-Instructions for Yarra Clients&nbsp;Under ConstructionSorry, this section is still missing. Please check again soon.</description>
</item>
<item>
<title>Administration</title>
<link>http://yarra-framework.org/logserver/administration/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/logserver/administration/</guid>
<description>&nbsp;Administration&nbsp; Administration of Yarra LogServer is done with a web-based interface (&ldquo;LogViewer&rdquo;), which normally runs on port 4444 (e.g., https://localhost:4444 when opening the browser directly on the server). It is recommended to use a modern web browser (e.g., Chrome) when working with LogViewer.
&nbsp; Accounts New user accounts can be created on the login page by going through the Registration procedure. However, new accounts are disabled by default and need to authorized by an administrator.</description>
</item>
<item>
<title>Configuration</title>
<link>http://yarra-framework.org/server/configuration/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/configuration/</guid>
<description>&nbsp;Directory StructureAfter the initial installation, the YarraServer folder has the following directory structure:
Path Purpose fail/ Target folder for failed reconstruction tasks finished/ Target folder for completed tasks (if data should be kept) install/ Folder with supplementary files for the installation log/ Folder for log files modes/ Folder with definitions of reconstruction modes modules/ Folder with binaries of core processing modules (shipped with Yarra) modules_user/ Folder with binaries of custom-developed modules queue/ Queue directory with incoming reconstruction tasks webgui/ Folder for the web-based user interface work/ Working directory for temporary files during processing By default, these folders are local subfolders in the ~/yarra installation directory.</description>
</item>
<item>
<title>Development</title>
<link>http://yarra-framework.org/modules/development/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules/development/</guid>
<description>&nbsp;Implementing Custom ModulesImplementing new reconstruction modules in Yarra is easy. Yarra modules are essentially just Linux command-line calls with a defined set of arguments. In addition, a number of processing conventions exist. The modules can be implemented in any language running on the Ubuntu 16.04/18.04 operation system (compiled or scripted). The spectrum ranges from simple Matlab, Bash, or Python scripts – typically used for clinical evaluation of early prototypes – to performance optimized C++ or GPU-supported implementations.</description>
</item>
<item>
<title>FAQ</title>
<link>http://yarra-framework.org/overview/faq/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/overview/faq/</guid>
<description>&nbsp;Frequently Asked Questions&nbsp; General &nbsp; If I only want to collect raw-data from clinical scans, do I need to install a Linux server?No. If you only want to collect raw-data without automatic offline reconstruction, then you can simply use the Yarra RDS client on your MR systems without need to install a Linux server. The data can be stored on any network share or USB drive. Are you planning to support other MRI vendors besides Siemens?</description>
</item>
<item>
<title>ORT Client</title>
<link>http://yarra-framework.org/clients/ort/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/clients/ort/</guid>
<description>&nbsp;UsageThe ORT client is the Yarra client for submitting reconstructions tasks from the consoles (host computer) of Siemens MRI systems. When started, the client will automatically connect to the Yarra server and read the list of configured reconstruction modes (see this page on how to configure of reconstruction modes).
Afterwards, it will show the main application window where all recent patient exams are listed that match to the defined reconstruction modes (i.</description>
</item>
<item>
<title>PACSTransfer</title>
<link>http://yarra-framework.org/modules_core/pacstransfer/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules_core/pacstransfer/</guid>
<description>Purpose Sends all reconstructed DICOM images to one or multiple DICOM nodes (PACS or DICOM workstation). Requires installation of the OFFIS dcmtk package on the server.
Usage PACSTransfer [mode file] [directory with DICOMs] Typical call:
[Transfer]Bin=%bd/PACSTransferArgs=%mc %td Configuration In .mode file:
[PACSTransfer]AEC=#AEC of PACSIP=#IP of PACS, e.g. 10.142.23.54Port=#Port of PACS, e.g. 104AET=#AET to be used, e.g. YARRA If the images should be sent to multiple DICOM nodes (up to 20), add to .</description>
</item>
<item>
<title>WebGUI</title>
<link>http://yarra-framework.org/server/webgui/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/webgui/</guid>
<description>&nbsp;IntroductionYarra provides a convenient web-based user interface for YarraServer (WebGUI), which can be used to monitor, control, and configure the server. The WebGUI is accessible from every web browser, including smartphones, by using the server address as URL with extension :8080, e.g. 192.168.56.101:8080. The port can also be changed to a different number. The WebGUI offers a user authentication system with different access levels, ranging from view-only monitoring of the reconstruction queue to full configuration rights for the YarraServer.</description>
</item>
<item>
<title>IDEA Hints</title>
<link>http://yarra-framework.org/developer/idea/</link>
<pubDate>Mon, 03 Jun 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/developer/idea/</guid>
<description>&nbsp;IDEA Developer Notes&nbsp; Installing VE11D Make sure to update MARS to the version supplied with VE11D. Otherwise, the linker will have unresolved functions. The regtarg tool seems broken. Targets have to be manually added to the Windows and Linux target lists in (C:\MIDEA\N4_VE11D_LATEST_20180608\MedMake\cfg\n4 and \n4linux). When running the MARS VM as &ldquo;external VM&rdquo; (i.e. managed manually via a separate VirtualBox installation):
Recreate the VM from scratch and import the 2 VDI disks (don&rsquo;t just use the existing vbox files - will result in kernal panic and and endless boot loop).</description>
</item>
<item>
<title>Data Visualization</title>
<link>http://yarra-framework.org/logserver/redash/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/logserver/redash/</guid>
<description>&nbsp;Data Visualization with RedashWhile the included Yarra LogViewer provides access to all collected data in tabular form, it is often desired to visualize data or to perform advanced queries. This can be done with Redash, which is a web-based open-source tool for creating SQL-driven dashboards.
More information on Redash
Please use only the Self Hosted Open Source version of Redash. Do not use the hosted cloud version, as this would transfer sensitive data to external cloud servers.</description>
</item>
<item>
<title>Manual Control</title>
<link>http://yarra-framework.org/server/usage/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/usage/</guid>
<description>&nbsp;Starting and Stopping the Server&nbsp; In most use cases, the YarraServer process is controlled via the WebGUI. However, it is also possible to control the server using command-line tools. &nbsp;
If Running as Linux Daemon When the YarraServer has been installed as daemon (recommended and described here), the YarraServer can be started using a terminal shell (as user yarraserver) and typing:
sudo systemctl start yarra The server is now running in the background.</description>
</item>
<item>
<title>Packaging</title>
<link>http://yarra-framework.org/modules/packaging/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/modules/packaging/</guid>
<description>&nbsp;Module PackagingModules can be packaged by creating a ZIP archive of all files. In addition, a manifest file has to be placed inside the ZIP file.
When installing a module through the WebGUI, the ZIP file will be extracted into a subfolder under /yarra/modules_user. The installation folder is named according to the filename of the manifest file that is contained in the ZIP archive. Thus, it is possible to append a version number to the ZIP file (e.</description>
</item>
<item>
<title>SAC Client</title>
<link>http://yarra-framework.org/clients/sac/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/clients/sac/</guid>
<description>&nbsp;UsageThe SAC client is intended for installation on stand-alone Windows workstations and can be used to submit measurement files for reconstruction that have been previously saved either manually using the Siemens TWIX tool or automatically using the Yarra RDS client.
To send a task, click on the “Select…” button and choose the .dat (TWIX) file that you want to reconstruct. The client will show the patient name and pre-select the reconstruction mode according to the protocol tags contained in the protocol name.</description>
</item>
<item>
<title>Source Code</title>
<link>http://yarra-framework.org/download/sourcecode/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/download/sourcecode/</guid>
<description>&nbsp;Open Source AccessThe Yarra Framework is an open-source project. The code for all components of Yarra is publicly hosted on GitHub. Click the buttons below to get to the repositories of the individual components. The source code is provided under the GNU General Public License (GPL).
If you want to build Yarra binaries yourself, you can find setup instructions for the build environmnet here.
&nbsp; &nbsp;Yarra Client Page on GitHub&nbsp;Yarra Server Page on GitHub&nbsp;Yarra WebGUI Page on GitHub&nbsp;Yarra LogServer Page on GitHub&nbsp;Yarra Archive Search Page on GitHub&nbsp;Yarra FileMover Page on GitHub&nbsp;Yarra Link Page on GitHub</description>
</item>
<item>
<title>Example Queries</title>
<link>http://yarra-framework.org/logserver/queries/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/logserver/queries/</guid>
<description>&nbsp;Sample LogServer Queries&nbsp;Under ConstructionSorry, this section is still missing. Please check again soon.</description>
</item>
<item>
<title>Resources</title>
<link>http://yarra-framework.org/download/resources/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/download/resources/</guid>
<description>&nbsp;Additional Material&nbsp; ISMRM 2019 Educational Session on Open-Source Software Tools &nbsp; &nbsp;Whitepaper on Concept&nbsp;Overview Slides&nbsp;Tutorial Slides on Offline Reconstruction&nbsp; </description>
</item>
<item>
<title>RDS Client</title>
<link>http://yarra-framework.org/clients/rds/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/clients/rds/</guid>
<description>&nbsp;IntroductionThe Yarra RDS client is a service that runs in the background on the host computer of Siemens MRI systems and can be used to automatically collect the raw data (Twix data) of certain scans and to transfer the data to a network location (or disk drive). RDS is part of the Yarra package for historical reasons and does not directly interact with the Yarra server. However, the data collected with RDS can later be submitted to a Yarra server using the SAC client.</description>
</item>
<item>
<title>Reconstruction Modes</title>
<link>http://yarra-framework.org/server/modes/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/modes/</guid>
<description>&nbsp;Defining Reconstruction ModesAdding a new reconstruction mode to YarraServer involves two steps:
A new .mode file needs to be created in the yarra/modes directory and named according to the internal ID of the reconstruction mode. The mode needs to be added to the list of available modes, read by the Yarra clients from the file yarra/queue/YarraModes.cfg. With recent versions of Yarra, this step is normally done via the Yarra WebGUI.</description>
</item>
<item>
<title>YarraCloud</title>
<link>http://yarra-framework.org/overview/yarracloud/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/overview/yarracloud/</guid>
<description>&nbsp;Cloud-Driven Reconstruction ServiceYarraCloud is a cloud-based service that allows performing offline reconstructions without the need to install local Yarra servers. YarraCloud has been built on a containerized version of the YarraServer binary and integrates seamlessly into the Yarra ORT and SAC clients. It enables centers that don&rsquo;t have the funds available for purchasing an on-premise server or that don&rsquo;t have the technical expertize to operate a Linux server to perform offline-reconstructions through a pay-per-use model.</description>
</item>
<item>
<title>YarraLink</title>
<link>http://yarra-framework.org/addons/yarralink/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/addons/yarralink/</guid>
<description>&nbsp;IntroductionXA Software Please take a look at this blog post about an updated approach for the YarraLink sequence, intended for newer XA software versions.
Installing or copying executables on the host computer of Siemens MR systems is officially not permitted by Siemens Healthcare. Therefore, installing the Yarra Client Package on the host computer of a Siemens MR system is at the user’s own risk.
As a “legally safe” alternative, it is possible to use the YarraLink sequence, which is a pseudo-sequence written in the Siemens IDEA framework that, instead of performing an MRI scan, opens the Yarra ORT client.</description>
</item>
<item>
<title>Notifications</title>
<link>http://yarra-framework.org/server/notifications/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/notifications/</guid>
<description>&nbsp;Notification EmailsThe YarraServer will send notification emails on completion or failure of tasks (prerequisites are that the sendmail package is installed and that notifications are enabled in the server configuration). Completion notifications will be sent to a) receivers listed in the Yarra client during submission and b) receivers listed in the reconstruction-mode file. Failure notifications will be, in addition, also sent to those receivers listed in the server configuration file under Options/ErrorMail.</description>
</item>
<item>
<title>Load Balancing</title>
<link>http://yarra-framework.org/server/loadbalancing/</link>
<pubDate>Fri, 15 Jun 2018 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/server/loadbalancing/</guid>
<description>&nbsp;Routing and Load BalancingIf multiple Yarra servers have been installed in a network, it is possible to route certain reconstruction tasks to dedicated servers as well as to distribute the task load across multiple servers. &nbsp;
&nbsp;Server List FileTo use multiple servers with the Yarra ORT client, it is necessary to create a server-list file named “YarraServerList.cfg” in the queue directory of the Yarra server that has been entered in the ORT configuration (preferably, the file should be placed in the queue directory of all Yarra servers and kept consistent).</description>
</item>
<item>
<title>Migration to GitHub</title>
<link>http://yarra-framework.org/blog/github_migration/</link>
<pubDate>Fri, 19 Jul 2024 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/github_migration/</guid>
<description>This week, we migrated Git all source code from Bitbucket to GitHub. The Yarra source code can now be found under the Yarra Organization page https://github.com/yarra-framework. The repositories on Bitbucket will continue to exist as backup, but will not be updated anymore. If you are actively working with the Yarra source code, make sure to change the remote location of the repository to GitHub.
This can be done with the following commands:</description>
</item>
<item>
<title>Client Package 0.65</title>
<link>http://yarra-framework.org/blog/client_065/</link>
<pubDate>Tue, 11 Jun 2024 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_065/</guid>
<description>A new version of the Yarra Client package has been released (version 0.65b1), which adds support for the scanner software versions XA51, XA60, and XA61. Moreover, the ORT client now keeps track of which cases have been sent to the Yarra server. This information is shown as additional column in the UI.
The version is now available in the Download section.</description>
</item>
<item>
<title>New Support Forum</title>
<link>http://yarra-framework.org/blog/new_forum/</link>
<pubDate>Tue, 14 Feb 2023 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/new_forum/</guid>
<description>Due to recent changes to the Gitter messaging service, we have migrated the Yarra Support Forum to GitHub Discussions. You can access the new forum using this link. You just need a GitHub account to participate in the discussions. Questions in the former Gitter forum will not be answered anymore.</description>
</item>
<item>
<title>Yarra on XA Scanners</title>
<link>http://yarra-framework.org/blog/running_on_xa/</link>
<pubDate>Wed, 19 Oct 2022 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/running_on_xa/</guid>
<description>Background The &ldquo;Numaris X&rdquo; or &ldquo;XA&rdquo; software, which is running on the newest MAGNETOM scanners (Vida, Sola) and on upgraded scanners (Prisma, Skyra, Aera, &hellip;), introduced several security or &ldquo;system hardening&rdquo; mechanisms, including the Windows Kiosk mode and the requirement to enter the admin password whenever starting an application outside of SyngoMR. While it is generally good news that the security has been improved, these new protections make it difficult to use Yarra routinely because they require leaving the Kiosk mode after each system reboot and require entering the admin password repeatedly when launching the Yarra RDS or ORT client.</description>
</item>
<item>
<title>Introducing Yarra Diagnostics</title>
<link>http://yarra-framework.org/blog/yarradiagnostics/</link>
<pubDate>Tue, 18 Oct 2022 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/yarradiagnostics/</guid>
<description>The Yarra Client package now comes with a new tool called Yarra Diagnostics, which helps identifying various problems that can occur on the scanner side. The tool can either be started using the Windows Explorer (by clicking the icon Diagnostics.exe) or from the ORT Client (by right-clicking on the orange Yarra logo and selecting &ldquo;Diagnostics&hellip;&rdquo;).
When clicking the &ldquo;Run Diagnostics&rdquo; button, the tool conducts a series of tests to identify installation and configuration issues as well as collects system information that may be helpful for resolving Yarra-related problems.</description>
</item>
<item>
<title>Client Package 0.62</title>
<link>http://yarra-framework.org/blog/client_062/</link>
<pubDate>Mon, 17 Oct 2022 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_062/</guid>
<description>A new version of the Yarra Client package has been released (version 0.62), which provides multiple improvements and new features:
Added support for scanner software versions XA40A and XA50A New Yarra Diagnostics tool, which analyzes various configuration issues on scanners that may impact different Yarra components (network connectivity, DNS configuration, etc) RDS: New option to buffer exported raw data on a different location than the C:\ drive, which may be needed when exporting large scans on scanners with a small hard drive Updated UI with dark-mode design, which blends better into the user interface of XA-line scanners The version is now available in the Download section.</description>
</item>
<item>
<title>Client Tools 0.5</title>
<link>http://yarra-framework.org/blog/clienttools_v5/</link>
<pubDate>Tue, 22 Mar 2022 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/clienttools_v5/</guid>
<description>A new version of the Yarra Client Tools (YCT) has been released (version 0.5).
This version adds support for anonymizing Twix files from XA30 and XA31. Moreover, the yct_getseqparams tool now offers an &ldquo;indexing&rdquo; function that collects parameters from all Twix files in a folder (and its subfolders) and creates a summary CSV file. This can be helpful for identifying protocol inconsistencies within collections of raw-data files or for ensuring that all raw-data files have been saved with adjustment data.</description>
</item>
<item>
<title>mercure DICOM Orchestrator</title>
<link>http://yarra-framework.org/blog/mercure/</link>
<pubDate>Sun, 20 Feb 2022 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/mercure/</guid>
<description>If you are looking for an open-source solution to automate tasks when working with DICOM images, such as running image-processing algorithms or routing studies, please check out Yarra&rsquo;s sister project &ldquo;mercure&rdquo; (think of it as &ldquo;Yarra for DICOMs&rdquo;). You can learn more about mercure in the video embedded below or by visiting the mercure homepage at: http://mercure-imaging.org/docs
&nbsp; &nbsp;</description>
</item>
<item>
<title>Client Package 0.60</title>
<link>http://yarra-framework.org/blog/client_060/</link>
<pubDate>Sat, 25 Dec 2021 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_060/</guid>
<description>A new version of the Yarra Client package with minor improvements has been released (version 0.60).
The version is now available in the Download section.</description>
</item>
<item>
<title>Yarra Presented at ESMRMB 'MRI Together' Workshop </title>
<link>http://yarra-framework.org/blog/esmrmb/</link>
<pubDate>Tue, 21 Dec 2021 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/esmrmb/</guid>
<description>The Yarra Framework has recently been presented at the ESMRMB Workshop &ldquo;MRI Together&rdquo;. If you are interested to learn about the background why we developed Yarra and how we are using it in our clinical practice, take a look at the talk &ldquo;Distributed Image Reconstruction in Academia&rdquo;
&nbsp; </description>
</item>
<item>
<title>Client Package 0.59 with Support for XA30/XA31</title>
<link>http://yarra-framework.org/blog/client_059/</link>
<pubDate>Fri, 17 Dec 2021 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_059/</guid>
<description>A new version of the Yarra Client package has been released (version 0.59) that adds support for the Siemens software versions XA30A and XA31A. In addition, RDS now has an option to disconnect from the network share after the update has been completed.
The version is now available in the Download section.</description>
</item>
<item>
<title>Client Tools 0.4</title>
<link>http://yarra-framework.org/blog/clienttools_v4/</link>
<pubDate>Fri, 13 Aug 2021 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/clienttools_v4/</guid>
<description>A new version of the Yarra Client Tools (YCT) has been released (version 0.4). Please replace old versions of the Yarra Client Tools with this latest release, as it contains improvements of the anonymization tool.
The version is now available in the Download section.</description>
</item>
<item>
<title>Client Tools 0.3</title>
<link>http://yarra-framework.org/blog/clienttools_v3/</link>
<pubDate>Thu, 22 Jul 2021 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/clienttools_v3/</guid>
<description>A new version of the Yarra Client Tools (YCT) has been released (version 0.3). Please replace old versions of the Yarra Client Tools with this latest release, as it contains improvements of the anonymization tool.
The version is now available in the Download section.</description>
</item>
<item>
<title>Client Package 0.58</title>
<link>http://yarra-framework.org/blog/client_058/</link>
<pubDate>Sun, 26 Jul 2020 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_058/</guid>
<description>A new version of the client package has been released (version 0.58) that adds support for the Siemens software versions XA20A and XA20B. In addition, several minor bugs have been fixed.
The version is now available in the Download section.</description>
</item>
<item>
<title>Migration to Git</title>
<link>http://yarra-framework.org/blog/gitmigration/</link>
<pubDate>Wed, 12 Feb 2020 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/gitmigration/</guid>
<description>We are currently migrating our source code repositories from Mercurial to Git. This is necessary because BitBucket, which we are using as provider for hosting the Yarra source code, is ending support for Mercurial. Some of the repositories might be temporarily unavailable during the time of conversion. After the migration, the repositories will have the same name (slug) and same website URLs, but you will need to use Git if you want to checkout the code.</description>
</item>
<item>
<title>Upgrade Your WebGUI</title>
<link>http://yarra-framework.org/blog/upgrade_webgui/</link>
<pubDate>Thu, 07 Nov 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/upgrade_webgui/</guid>
<description>If you are still running an older version of the Yarra WebGUI, please update it to the latest version (version 0.97). We are soon shutting-down our old internet domain yarra.rocks and by updating the WebGUI to the latest version, you will continue to receive the latest news and update information right into the WebGUI of your YarraServer. In addition, the latest version of the server package also provides the much-needed resume functionality for tasks that failed during post-processing or transfer steps (so that the reconstruction does not need to be performed again).</description>
</item>
<item>
<title>Client Package 0.55</title>
<link>http://yarra-framework.org/blog/client_055/</link>
<pubDate>Wed, 06 Nov 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_055/</guid>
<description>A new version of the client package has been released (version 0.55) that now also supports the Siemens software version VE11S. Moreover, the SAC client now allows sending additional files along with the task, enabling to send, e.g., separate calibration data to the reconstruction module.
The version is now available in the Download section.</description>
</item>
<item>
<title>Hermes DICOM Router</title>
<link>http://yarra-framework.org/blog/hermes/</link>
<pubDate>Mon, 02 Sep 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/hermes/</guid>
<description>Looking for a flexible and powerful DICOM Router to integrate your image-analysis prototypes or AI solutions into your clinical workflow? Check out Yarra&rsquo;s sister open-source project &ldquo;Hermes Router&rdquo;, which is now publicly available:
http://hermes-router.github.io</description>
</item>
<item>
<title>Matlab GRASP Module</title>
<link>http://yarra-framework.org/blog/matlab_grasp/</link>
<pubDate>Mon, 15 Jul 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/matlab_grasp/</guid>
<description>A new Matlab-based public version of the GRASP reconstruction algorithm has been released, which integrates into the Yarra offline-reconstruction pipeline. The module has been parallelized using Matlab&rsquo;s Parallel Computation Toolbox and achieves reconstruction speed in the same magnitude as our C++ implementation of the algorithm.
The algorithm can be downloaded on the User Modules page. Please note that Matlab R2016a or newer is required.
The required pulse sequence for GRASP scans, known as &ldquo;RAVE&rdquo; or &ldquo;Radial-VIBE&rdquo; sequence, can be obtained from us after filing a C2P agreement with Siemens.</description>
</item>
<item>
<title>Yarra Client Tools</title>
<link>http://yarra-framework.org/blog/clienttools/</link>
<pubDate>Fri, 05 Jul 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/clienttools/</guid>
<description>The Yarra Client Tools (YCT) are now available for download. Yarra Client Tools are small command-line tools that help with processing Siemens Twix files. They provide functions for batch anonymization, protocol extraction, and for displaying individual scan parameters. The package should be extracted into the installation folder of the Yarra Client package.
The version is now available in the Download section.</description>
</item>
<item>
<title>Client Package 0.54</title>
<link>http://yarra-framework.org/blog/client_054/</link>
<pubDate>Thu, 27 Jun 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/client_054/</guid>
<description>A new version of the Yarra Client Package has been released (version 0.54). This version offers improved support for the scanner software XA11A and XA11B.
Starting with version XA11A, Siemens has changed the Windows security policies such that even the execution of white-listed applications requries entering the password of the administrator account each time. This can be cumbersome when submitting offline-reconstruction tasks. Therefore, we added an alternative mechanism for launching the Yarra ORT client via a menu that opens by right-clicking on the Yarra icon.</description>
</item>
<item>
<title>New Release of YarraServer and Client Package</title>
<link>http://yarra-framework.org/blog/release_june19/</link>
<pubDate>Tue, 18 Jun 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/release_june19/</guid>
<description>New versions of the YarraServer and Yarra Client packages have been released.
Yarra Client 0.53 adds support for our YarraCloud service. Moreover, new software versions of the Siemens scanners are supported, including VB19B, VE11D, VE11E,VE12U, XA11A, and XA11B. To use the Yarra Client on scanners with the XA software line (MAGNETOM Vida and Sola), it is necessary to install software certificates. Please contact us to obtain these certificates.
YarraServer 0.97 has now been built using an Ubuntu 16.</description>
</item>
<item>
<title>Support</title>
<link>http://yarra-framework.org/embed_support/</link>
<pubDate>Thu, 23 May 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/embed_support/</guid>
<description></description>
</item>
<item>
<title>Workshop at ISMRM 2019</title>
<link>http://yarra-framework.org/blog/ismrm2019/</link>
<pubDate>Fri, 10 May 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/ismrm2019/</guid>
<description>We will present Yarra in the Weekend Educational Session on Open-Source Software Tools that will take place at the ISMRM 2019 Meeting in Montreal. Roy Wiggins will give an overview talk at 11:00am and give a practical demonstration on how reconstruction algorithms can be integrated into Yarra at 1:30pm, 2:20pm, and 3:10pm.
You can find the training material also in the Resources section.
ISMRM Educational Session on Open-Source Software Tools</description>
</item>
<item>
<title>End of support for Ubuntu Version 12.04 and 14.04</title>
<link>http://yarra-framework.org/blog/end-of-1204/</link>
<pubDate>Fri, 03 May 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/end-of-1204/</guid>
<description>We decided to end the support We decided to end the support of the Ubuntu version 12.04 LTS and 14.04 LTS. These two versions have now reached the end-of-life date and will not receive security updates anymore. Moreover, there are library incompatibilities that would require us to provide separate binaries. The configuration steps have also changed due to Ubuntu&rsquo;s migration from Upstart to systemd. Therefore, we decided to drop support for these outdated Ubuntu versions and we encourage all users to upgrade their servers to either Ubuntu 16.</description>
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<item>
<title>New Website for Yarra</title>
<link>http://yarra-framework.org/blog/new-website/</link>
<pubDate>Tue, 26 Mar 2019 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/blog/new-website/</guid>
<description>We finally managed to create a new website for the Yarra framework and hope to provide more up-to-date information on Yarra going forward. Currently, we are still in the process of migrating some remaining content from our old website, but this should be completed soon.
For reference, the old website is still available under this link. Note, however, that the old website will not be updated anymore, so that the information provided there can be outdated.</description>
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<item>
<title>Disclaimer</title>
<link>http://yarra-framework.org/disclaimer/</link>
<pubDate>Thu, 01 Oct 2015 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/disclaimer/</guid>
<description>DisclaimerThe Yarra framework is provided free of charge for use in research applications. It must not be used for diagnostic applications. The authors take no responsibility of any kind for the accuracy or integrity of the created data sets. No data created using the framework should be used to make diagnostic decisions.The Yarra framework provided through this website, including all of its software components, comes without any warranties.</description>
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<item>
<title>License</title>
<link>http://yarra-framework.org/license/</link>
<pubDate>Thu, 01 Oct 2015 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/license/</guid>
<description>License InformationThe Yarra framework is provided free of charge for use in research applications. It must not be used for diagnostic applications. The author takes no responsibility of any kind for the accuracy or integrity of the created data sets. No data created using the framework should be used to make diagnostic decisions.The Yarra framework, including all of its software components, comes without any warranties. Operation of the software is solely on the user’s own risk.</description>
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<item>
<title>News</title>
<link>http://yarra-framework.org/embed_news/</link>
<pubDate>Thu, 01 Oct 2015 00:00:00 +0000</pubDate>
<guid>http://yarra-framework.org/embed_news/</guid>
<description></description>
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