Yarra Framework developed by the Center for Advanced Imaging Innovation and Research (CAI²R) at NYU School of Medicine.
tutorial (ppt) from resources page
▪ Background service on scanner consoles (“Yarra RDS”) ▪ Automatically exports raw data every night … ▪ Collection of utilities that help with clinical evaluation ▪ “Batch Processor” for integrating prototypes clinically ▪ Data transport, task management, monitoring, etc. ▪ Complements MRI reconstruction frameworks
Distribution of tasks to multiple servers possible
but through multiple Yarra servers(?). Could write sbatch/slurm wrapper. Only one job at a time – transfer back happens when job finishes.
https://s3.amazonaws.com/download.yarraframework.com/doc/ISMRM19_Tutorial.pdf
▪ YarraServer processes 1 task per time (“max-out resources”) ▪ Many scans → tasks waiting in queue
Yarra Cloud designed for AWS. uses Elastic computer.
https://yarra-framework.org/clients/installation/
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’.
https://yarra-framework.org/modules/user/ https://yarra-framework.org/modules/development/
- Can use Berkeley Advanced Reconstruction Toolbox (https://mrirecon.github.io/bart/)
- GRASP (Golden-angle radial sparse parallel MRI, 2014 Feng et al Magn Reson Med)
https://yarra-framework.org/addons/yarralink/ “YarraLink sequences binaries”
- requires IDEA license
When the exam program is executed during a patient examination, the Yarra ORT client will automatically open in the moment when the YarraLink sequence step is reached. Usage of the client is identical to the description provided in the ORT documentation. During the first start of the client, the configuration dialog will appear.
https://yarra-framework.org/clients/
| ort | client for submitting reconstructions tasks from the consoles |
| sac | The 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. |
| rds | 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. |
The Update Rule setting determines when the raw data is saved and transferred:
- On Startup: The update will be performed after the scanner is turned on and while the RF amplifier warms up. This setting should be used for MR systems that are shut down in the evening.
- At Fixed Time: The update will be performed at a certain time. Up to three update times can be defined. This setting should be used for systems that are not shut down in the evening, so that the update can be performed during the night.
- Periodically: The update will be performed periodically within certain time frames. This setting can be useful for systems that are used all day.
- Only Manually: The update will be performed only on manual trigger. To perform an update, open the main dialog by clicking on RDS.exe (or on the short-cut icon in the “Startup” folder) and clicking on “Transfer Now”. Alternatively, the update can be triggered with a separate icon in the Start menu (see optional installation steps).
- On Startup and at Fixed Time: With this setting, the raw data is transferred either when the scanner is turned on or at a certain time. It should be used on systems that are sometimes shutdown and sometimes run throughout the night. This rule is now the default setting for the update rule
https://yarra-framework.org/overview/faq/
For our GRASP reconstructions, we are typically using servers with 2x 16core Intel Xeon CPUs and 256 GB of RAM.
That’s close to what we have on local HPC!
free -g | awk '(NR==2){print $2}'
grep -ic processor /proc/cpuinfo| 251 |
| 16 |
Yarra River runs through Melbourne (Australia) [host city of 2012 ISMRM Annual Meeting, inception of software]