Overview - FAQ

 Frequently Asked Questions

 

General

 
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?
We would like to. However, at the moment, we are all working at centers that only have Siemens equipment. This makes it difficult to develop clients for other vendors. However, if you are interested in supporting this process, please reach out to us.
Do you support the ISMRMD format?
Yarra does not directly support the ISMRMD format, but there is nothing that stops you from using it. It is possible to launch a Twix-to-ISMRMD converter as preprocessing step, so that the reconstruction module gets the data in the ISMRMD format.
Is Yarra FDA approved?
No, it is not. Yarra is a pure research tool that facilitates bringing research techniques into clinical practice, but it is not meant to be used as a routine medical product.
How can I get help?
Please use our Gitter Channel to get in touch (see the Support page). Due to limited time, we cannot answer all personal emails that we receive.
Why is it called Yarra?
The Yarra River runs through Melbourne (Australia), along the convention center where the 2012 ISMRM Annual Meeting took place. That's where the idea for developing the framework came up. And because we enjoyed the ISMRM in Melbourne a lot, we decided to call it Yarra.
 

Clients

 
The client wont't start on the XA software. What can I do?
First, make sure that you have installed our Windows software certificates. Contact us to obtain the certificates and installation instructions. Second, on version XA11A or newer, programs can only be executed as administrator. Thus, you need to right-click on the icon and select 'Run as administrator'. When creating shortcuts, make sure to check the option 'Run as administrator' in the 'Advanced...' section of the shortcut properties.
The client wont't start on the VE/VD software. What can I do?
Make sure that you go through the white-listen procedure using the MREmbeddedControlUI tool. It is first necessary to set the scanner to 'Update' mode, then copy the files onto the scanner (if you copy prior to activating the 'Update' mode, the binaries won't be white-listed), and execute the binaries once. Afterwards, make sure to set the scanner back to mode 'Enabled'.
What is the best time to send tasks for offline reconstruction?
We usually initiate the task submission before going into the scanner room to take the patient from the table. In this way, the transfer is usually finished when returning to the scanner console.
 

Server

 
Where can I find the required server specifications?
Yarra itself is very flexible and should run on every Ubuntu Linux machine. The requirements largely depend on the reconstruction modules that should be executed. For our GRASP reconstructions, we are typically using servers with 2x 16core Intel Xeon CPUs and 256 GB of RAM.
Does YarraServer also run on a Virtual Server (VM)?
Yes! That's what we are doing for our development work and also in production. Whether it makes sense to run it on a virtual or physical server depends on the specific reconstruction that should be performed. For very demanding algorithms, it might make more sense to use a physical server while virtual servers offer the flexibility of cloning servers in short time.
Can YarraServer run as Docker container?
Yes, that is generally possible. However, since the data exchange is done via an SMB share (provided by Samba), it would be necessary to install Samba either as a second container or into the YarraServer container, and to properly configure it so that the share is accessible from outside the host system. We are not sure if setting up such configuration would be faster than directly installing it on a clean Ubuntu server or inside one VM.
 

LogServer

 
Why does my scanner need to have a DNS entry?
When using Yarra for clinical workflow monitoring, PHI will be (securely) transmitted to the Logsever. We want to ensure that under no circumstances data can leak out of the hospital network due to a misconfiguration of the service. Therefore, the Yarra RDS client checks on the local DNS server if the MR scanners host and LogServer host are known, and if they are in the same domain. Only if both is true, the data is transmitted. It is possible to disable this mechanism in the source code of the client. We are not providing binaries with disabled DNS check, so you would have to compile the client yourself. However, it's better to configure DNS entries for your scanners.
Can I use other tools for the data analysis than Redash?
Yes! Yarra LogServer stores the data in a standard Postgres SQL database. Thus, any BI software that supports Postgres could be used for the visualization. Cloud-based tools should NOT be used because the database contains PHI, such as the patient name. Therefore, the data should under no circumstances be analyzed or transferred to an external service.