Dario Bosch
@dabosch
Hi,
I'm working together with @BlakeGFitch and have a question regarding RDS.
I noticed that RDS first exports the data files to a local folder (queue) before moving them to the specified network drive. Especially for large data files that overall process takes significantly longer than directly exporting to the network drive using twix. Is there a reason why no direct export is done? Are there plans to change that in the future, or add it as an option?
On our system the local hard drive seems to be slower than the network drive so I would prefer a direct export.
Tobias Block
@tblock79
@dabosch Hi Dario, The scanners cannot start new scans while data is being exported. Therefore, Yarra is first writing all data to the C: drive and then moving it to the network share (during which scanning can proceed). Also, this allows buffering data if the network share is temporarily unavailable. It would very much surprise me if the network share is faster than the local hard drive (I think generally, this is not the case). However, if you want to test it, you could a) install your Yarra client on the network share instead of the local drive (because it's buffering the files in the "queue" folder under the installation path) or b) modify the code accordingly and rebuilt the client
Jeffrey Luci
@lucijj

Hello: I'm at the University of Texas at Austin. We have a Semens Vida running XA11B, and I understand we need to request a certificate. Could you please contact me and let me know what you need to issue one?

thank you,
Jeff Luci

BlakeGFitch
@BlakeGFitch
@tblock79 Hi Tobias, I hope social distancing is treating you well
I was wondering if an MR session produces several .dat files and for each, several dicom files how I can figure out which dicom files are associated to a specific .dat file
If you have any suggestions it would be most appreciated
BlakeGFitch
@BlakeGFitch
@tblock79 ... at the risk of being annoying, I figured I'd ping again to see if you were looking in after the Easter weekend.
Tobias Block
@tblock79
@BlakeGFitch Not aware that there is a unique ID in the raw data or DICOMs that allows you to make that association. You could probably look at the acquisition order or acquisition time but it could get fiddly
BlakeGFitch
@BlakeGFitch
@tblock79 Thanks and wow! I've been looking through fields with the others involved and we haven't found an answer. I guess perhaps time stamps might work but I was hoping not to go there.
ICUH
@ICUH
Hi @tblock79 I am trying to setup specification for server that will be running Yarra. I am in conundrum whether to use AMD or Intel processor.
I was wondering, if Yarra/Ubuntu will be okay to run on zen2 epyc. Or possibly virtualization is based on Intel VT. Thank you in Advance.
Tobias Block
@tblock79
Hi @ICUH, Yarra itself does not use any processor-specific instruction sets, so it should run on either AMD or Intel processors (our servers are a mix of both). It should also run in virtual environments (we have used it on VirtualBox, VMware, and Docker without problems). If the reconstruction modules that you are planning to use with Yarra have specific requirements, that needs to be taken into account of course
Johannes Töger
@johannestoger

Hi! I was really happy to find out about the Yarra project. Looks like a great package. I'm very thankful that it's freely available.

I have a question about the Raw Data Service (RDS). We have two clinical scanners where I'd like to use it to automatically extract research raw data, one on N4 E11C and one on NX A20A. How has stability and interference with clinical operations been so far? Any input from sites that have it installed?

Best,
Johannes Töger
Associate Senior Lecturer
Lund University, Sweden

Johannes Töger
@johannestoger
Correction - it's NX A20B actually.
Tobias Block
@tblock79
Hi Johannes, Currently NX20 is not supported yet, but hope to add that soon (can't access any MRI systems at the moment due to Covid-19). XA11 is supported (and VE11C of course too). We've been using RDS for many years in our center and have collected terabytes of raw data with it. I'd say it works very reliably. In our center, the scanners run over night. Therefore, we are doing the raw data transfer at night, so that there is no interference with the clinical operations. It's also possible to install Yarra LogServer to monitor RDS (so that you get alerts if there are problems with connecting to the network shares etc)
Johannes Töger
@johannestoger
@tblock79 OK, thanks! Sounds like I should give this a try then.
Johannes Töger
@johannestoger
@tblock79 I see that the source code is available -- what kind of adjustments would I need to do make it work on NX20?
Johannes Töger
@johannestoger
@tblock79 Hi again -- our local MRI techs want to know if Yarra RDS needs any form of write access to the RAID database, or if it's just reading. If it's just reading from the RAID, my life will be much easier.
Tobias Block
@tblock79
@johannestoger Hi Johannes, Yarra is just reading from the RAID -- there is no write access to the RAID. Actually, it's only calling the "RaidTool" which is an official command-line tool provided by Siemens that is part of the regular MR software.
@johannestoger To make adjustments for XA20, you would have to add entries into the files rds_runtimeinformation.h and rds_global.h. But it would be also important to check if any changes to the RaidTool have been made, so that the output format might be different (Siemens frequently makes changes to the output format). Will try to work on that in the next days and can check with you regarding testing
Johannes Töger
@johannestoger
@tblock79 OK, I see - good to know that it's read-only. Regarding XA20, please let me know how I can help.
Joshua van Amerom
@jfpva

Quick note that the html files are missing from Yarra Archive Search v0.14 download.

I recently installed it and took me a bit to figure out that was the case. Copied them from v0.13 to get the service up and running. Figured it was worth mentioning to help others, like me, who are using this add-on for the first time.

Also, while fairly obviously a typo, in the YAS installation notes there is command to enable the yarrawebgui service that should be the yaswebgui instead.

Thanks, once more, Tobias, Roy and all involved for their work on these tools.

Johannes Töger
@johannestoger
@tblock79 A question about Yarra RDS from our local tech staff: Yarra RDS first exports .dat files from the RAID to a temporary folder, and then transfers files to a network drive. Is the temporary folder automatically emptied, or do we need to do that manually? We don't want to end up in a situation where we fill up a disk with temporary files.
Tobias Block
@tblock79
@johannestoger The files are stored first on the local drive (to ensure that scanning is possible asap again), then transferred to a network destination, and then removed from the local drive. Thus, the hard drive should not fill up. If the network connection cannot be established for some time, files can "pile up" on the local drive. However, the Yarra RDS Client will stop exporting new files if the remaining disk space goes below a certain threshold (to make sure that the scanner operation is not put at risk). So far, we haven't encountered any problems in that regard
Tobias Block
@tblock79
@jfpva Thanks for pointing out these issues! Should all be fixed now.
pimpul
@pimpul
@tblock79 I have installed yarraserver on a local machine. Perhaps it's a naive question, but is it possible to perform GRASP reconstruction without RDS or SAC? I would only need to do a couple of reconstructions. I have the raw data (*.dat) copied from the scanner on a USB stick.
and we have a "difficult" ICT dept in our hospital, so it is difficult to open a port for the webgui to be accessed from another computer
Jeffrey Luci
@lucijj
We just upgraded our Vida to XA20A. Do you have an ETA for when that version will be ready? A best guess is fine, and would be helpful. THanks.
Tobias Block
@tblock79
@pimpul Yes, you could manually run the GRASP module from the bash shell, i.e. the binary called "GraspR" which is contained in the ZIP file. You would just need to provide the name of the Twix file, output folder etc. as commandline parameter (you can see the exact parameters on the website: http://yarraframework.com/modules/user/). There is a template ini file called default.ini in the ZIP file that you would have to modify (the GRASP module reads the reconstruction parameters from that file)
@lucijj I prepared a first test version that our techs are testing this week (we got the XA20A upgrade over the weekend). If they give green light, I will release it asap
Jeffrey Luci
@lucijj
@tblock79 , thanks! Will check back later for updates.
Joshua van Amerom
@jfpva

Hoping someone can expand on the notes about automatic loading of RDS during bootup of the scanner on the client package installation page.

We have RDS installed on two scanners (both VE 11). On one of them RDS starts up consistently, but on the other RDS appears to fail about once out of every four of five scanner reboots. I did see the note about adding a call to the RDS binary in the batch file as suggested at the bottom of the installation page, but am hoping to understand the issue more before making changes.

Thanks in advance for any insight.

Tobias Block
@tblock79
@jfpva In the past, we always just put the shortcut to RDS into the Windows Start folder. However, at some point (I believe after the VE11 upgrade) we noticed that RDS wasn't always starting on some of our scanners (although I never really figured out why -- possibly related to whether the techs go into "Advanced User" mode). The only way that I found to ensure that it's always loaded is to add it to that mentioned batch file. To do that, you just have to open that batch file with Notepad and append the command to start RDS at the end of the file. That seems to work reliably and it does not cause any problems. The only "downside" is that this modifies a "Siemens-provided file", so it might be good to make a backup first
Tobias Block
@tblock79
@lucijj Unfortunately, it turned out that there were upgrade problems last weekend, so the XA20A upgrade has been postponed to this weekend. Will let you know when I hear back from our techs
pimpul
@pimpul
@tblock79 thanks! I've been able to scan and reconstruct a first dataset
Andi Kwasniewski
@andiKwas
Hi, I am from Northwestern Medicine. How can I go about setting up a meeting with a Yarra support rep?
Tobias Block
@tblock79
@andiKwas Hi! There is no Yarra support rep. Yarra is non-commercial open-source software. You can post your questions here and we will try to answer them
OJCaster
@shnoru1
Hi Yarra Support Team @tblock79,
I've been working with Yarra RDS and it has been going well so far. However, I've been facing trouble while implementing our back up system because the RDS program will not start along with the system reboot. Also, MREmbeddedGui (and AdvancedUser) blocks the execution of RDS every reboot, which is a burden to our procedure. I'm wondering if there is any way to handle this. Thank you for the great framework.
Tobias Block
@tblock79
Hi @shnoru1 Which version of the MRI software are you working with? On VE11C, it should start automatically if you add RDS to the batch file MROrdinaryUser.bat as described on the Yarra Client Installation page. On NXA11 and NXA20, unfortunately, we didn't find a way yet to start RDS automatically while the system is in "kiosk" mode. Hence, here it's necessary that the techs manually leave the kiosk mode after each reboot.
OJCaster
@shnoru1
It turned out to be my mistake. I didn't copy the executable while Updated Mode was on. So, as written on the manual, the executable had not been whitelisted.
Thank you again for the great framework!
Joanna Kwon
@joannakwon_gitlab
Hi Tobias @tblock79, we are a team of engineers currently conducting research with a hospital. We were planning to utilized Yarra RDS to collect raw-data from the MRI systems in the hospital, but got push back from the hospital regarding security and stability of the software. Would you be able to share with us a few names of institutes or clinics/hospitals that have been happily using Yarra with no reported security/stability issues, apart from NYU? Such examples would be immensely helpful in persuading the board of this particular hospital in adopting a more efficient way of data collection. Thanks in advance!
Jeffrey Luci
@lucijj
@tblock79 , Is the problem with the NX20A just getting it to automatically start without closing the kiosk? If so, we're fine with operating it manually until a workaround can be found. Or, if you want me to help find ways, I have the time. Our scanner is not being used very much, and I now have approval to be in the lab. I'm happy to try to find solutions or beta test for you.
Tobias Block
@tblock79
@lucijj Hi! No, I don't think there is anything different from XA11. I think the version that we have now works fine on XA20. Will try to release it later today (or over the weekend)
@joannakwon_gitlab Will send you a few sites in a PM. In addition, you could also ask for experiences here in the discussion board
Tobias Block
@tblock79
@lucijj You can now find a new client version with support for XA20 in the download section.
Jeffrey Luci
@lucijj
Thanks a ton, Tobias @tblock79 ! I'll have time tomorrow to get it installed and tested.
jgalons
@jgalons
Hi Tobias, We have been using the yarralink sequence to transfer our data to an external shared drive along with "net use" cmd to mount the drive. Recently our hospital IT security team asked us to make sure that the mounted drive is disconnected after each transfer. Is there a way to automatically unmount the shared drive following a RDS data transfer? Thanks for your help
Tobias Block
@tblock79
@jgalons Hi! Are you using RDS or ORT to transfer the data (I am wondering because YarraLink is normally used with ORT)? With ORT, you can disconnect the network drive after the transfer. RDS does not support this at the moment, but if needed, we could add an optional command that is executed after the transfer (which could be used to execute "net use /delete")
jgalons
@jgalons
Thanks Tobias,
jgalons
@jgalons
I thought it was RDS that was used to transfer when using Yarralink ..We always got the RDS logo indicating that the data was being transferred after "checking" the Yarralink sequence. We have not used it for more than 14 months due to "restricting orders" issued by the new hospital owner IT security team. We are now cleared again. I will download the latest version of Yarralink and test it. Thanks again for your work!
Tobias Block
@tblock79
@jgalons It can well be that you are using YarraLink to start RDS (originally, it was intended to start ORT, but can be used to start RDS too). If you see the Yarra icon, that indicates that it's used to start RDS. Would be great if you could validate this. I will put the disconnect feature on the TODO list for the next RDS version. BTW, the YarraLink sequence has not been updated for a while, so your version is probably still current.