Tobias Block
@tblock79
@CKarmonik_twitter Hi Christof, Sure. Please send me your email address via PM and I will email it to you
usmanUCL
@usmanUCL
Hi Tobias, on XA11 system, we have issue that Yarra doesn't start automatically when we leave kiosk mode and the bat script is placed in the start up folder. The Yarra is installed on the local drive so it is not the issue of accessing the network. It gives the following message 'This program is blocked by group policy', is there a way around it? Thanks
Eric A. Borisch
@eborisch
Thanks for the tools; we've been using the RDS client to ease some research workflows. Do you when (if?) XA30 support is on the roadmap?
1 reply
Tobias Block
@tblock79
@usmanUCL Hmm, sorry, we haven't had that problem. On XA11, we actually put the shortcut to RDS.exe directly into the Windows Start menu. That seems to work as far as I can tell. I remember that we needed to use a trick from the command line in order to get to the folder with the Start menu (I think I just googled how to do that)
Tobias Block
@tblock79
@eborisch Hi Eric: We don't have any XA30 scanners here yet and I would like to test it first before claiming that it works on XA30. But I believe that we should get the update soon, so I don't think that it will take long until we will support it
conan-chen94
@conan-chen94
Hi Tobias, thanks so much for making such a great tool for the community. We are a new Siemens site and are looking into solutions to automatically transfer DICOMs off the scanner onto local servers on the network. From my reading, Yarra seems to be designed for transferring raw Twix data, not the DICOMs from the scanner - is that a correct statement? Under the Modules tab on yarraframework.com, I see there is a core module called "DriveTransfer" for sending DICOMs onto a network share, but is this for DICOMs created after custom off-line reconstructions on Twix data (as facilitated by Yarra), or DICOMs coming directly off the scanner? I also briefly looked at the sister tool of Hermes - for our use case, would Hermes sound like the better fit?
Tobias Block
@tblock79
@conan-chen94 Hi! That is correct. Yarra has been designed only to transfer / work with raw data from the Siemens scanners. And, yes, the DriveTransfer (or PACSTransfer) module is intended for sending the DICOMs reconstructed from the raw data to a storage location. If you want to transfer DICOMs to a local server, you could setup a DICOM receiver node using the "storescp" tool from the "OFFIS dcmtk" package (which is available for all operating systems) and to configure the MRI scanners to automatically push acquired DICOMs to this DICOM node. That might be all you need. Hermes would become useful if you want to distribute the DICOMs to different locations using routing rules, but you might not need that
ICUH
@ICUH
Hi @tblock79. Not sure, if you can answer the question regarding MATLAB GRASP module, or you can direct me to someone I can ask. I has issue with running the GRASP reconstruction using MATLAB due to phase oversampling. Raw data contains more partitions than image per slab, causing zerofill_Kz script to fail. (zerofill_Kz expects partitions <= image per slab) Counter-part C++ reconstruction method works fine with the raw data. (I guess, as far as I can extract from the log file, in c++, zerofill is ignored and number of slice are reduced after fft and coil sensitivity adjustment) Is that some what correct assessments? I can easily modify the matlab script to make it work, just need to know where to tackle the problem. Thanks in advance.
Tobias Block
@tblock79
@ICUH Hi! Sounds like you are using a sequence protocol with Slice Oversampling, i.e. more partitions are sampled than requested slices (to avoid in-folding artifacts). The function zerofill_Kz doesn't account for this option, so you need to adapt it accordingly. Basically, you need to arrange the data on a matrix with size corresponding to the acquired partitions, run a FFT along kz, and then cut away the outer partitions so that you end up with the correct number of slices (sort of the opposite to what is happening when Reduced Slice Resolution is used, which zeropads the kz data to the correct number of slices)
ICUH
@ICUH
Thank you for the insight @tblock79. I have made an adjustment in the matlab script to correct slice oversampling and works fine. Let me know if you want the modified script with you (it's only 6 lines changes). Thanks again.
Tobias Block
@tblock79
@ICUH Perfect! Yeah, would be great if you could share that (tobias.block@nyumc.org). Many thanks!!
Dario Bosch
@dabosch
I have an issue with RDS that breaks our workflow.
When exporting to a network drive, RDS uses the protocol as part of the file name. However, some symbols can be used in the protocol name, but may not be used in a Windows filename. So whenever a user names their scan something like "GRE A->P" RDS will fail to write the file. It will then also abort, not exporting any future scans.
According to Windows, the list of forbidden characters is \/:*?"<>|
1 reply
Is there a chance to sanitize the output filename in RDS from those symbols?
icuh
@beradinlim_gitlab
Hi @tblock79 Thanks in advance. Is it possible to input a custom data to c++ GRASP reconstruction and what format should it be? I have noticed there are options for sourcetype in option. In short, I would like to modified raw kspace data and use same header. But I don't have a tool to put raw kspace data back to dat file. (let me know if there is) In the side note, I have notice there is a significant difference between C++ GRAP and matlab reconstruction. It seems that there is some kind of step missing for matlab reconstruction to reduce noise or filter some kind. Let me know if that is case. Much Appreciated.
3 replies
hyunsoolee0503
@hyunsoolee0503
Hi @tblock79 We're using Yarra RDS on Vida (XA20a) at our site and it helped us a lot for efficient raw data export! We are planning to upgrade the software version to XA31a soon. I was just wondering if there's any plan for porting to XA31a and it would be great if I could learn the expected date for XA31a release. Thanks for your support as always. Best regards, Hyun-Soo
5 replies
marjoleinpiek
@marjoleinpiek
Hi @tblock79. We have been using Yarra RDS succesfully on our VE11C for a while now, very happy with how it works. Now we tried to install on our Siemens Sola (XA20A/B I think). It seemed to work, we could export data. However, after rebooting the scanner, part of the installation seemed to have dissappeared. Any help would be appreciated. Best regards, Marjolein Piek, Lund University, Sweden.
6 replies
marjoleinpiek
@marjoleinpiek
yarra_beforeReboot.jpg
yarra_afterReboot.jpg
Scott
@ScottHaileRobertson

I’m trying to use Yarra to backup TWIX data from multiple (12 total) scanners onto a single network drive (it’s a windows-based shared drive). Early on we ran into an issue where yarra’s “queue” folder was filling up and slowing down our scanners. Eventually, I realized that the shared drive will only allow us to connect from one scanner at a time (we are using the same login from each scanner), so once one scanner connected, all the others would not be able to connect, so the queue would grow and grow until the scanner slowed down. I could create individual users for each scanner, but that’s a pain to maintain yearly password changes for 12 scanners. Instead, I've learned windows will allow me to connect to the same shared network drive with the same user name so long as I don’t connect by ip address – instead I connect by a unique hostname from each scanner. So far this has solved the problem, but I’d like to take it a step further and try to minimize the amount of time each scanner is connected to the network drive. Is there a way to disconnect the network drive after backup?

Also, can someone explain the difference between putting "net use" networking commands into the "connect cmd" field on the "networking tab" vs in the "startup commands" tab?

Tobias Block
@tblock79
Hi Scott:
  • Yes, in the latest version of the client, you can enter a "disconnect cmd", which will be executed when the update has finished. This can be used to disconnect the network share (e.g., by putting "net use * /delete")
  • It's strange that only one scanner can connect to the share at the same time. Might be worthwhile reviewing the settings of the file server. In our case, we have ~ 30 scanners connecting to the same SMB share using the same account, and we don't see such problems.
  • There is an option in the RDS configuration to jitter the update the time to avoid that all scanners connect right at the same time. This might be helpful here.
  • The "connect cmd" on the networking tab is executed before each update and can be used to establish the connection with the network share where the raw data should be stored. The "startup commands" are executed only once when the RDS client boots. We are using it to restore other network connections after a reboot of the scanner (e.g., if someone has accidentally disconnected a network drive). In the past, we were doing this with a batch file in the Windows Startup folder, but Siemens disabled execution of batch files at some point. That's why we integrated the "startup commands" into RDS.
Scott
@ScottHaileRobertson
Great - I'll update our yarra version and use the disconnect cmd feature - Thanks! Also thanks for sharing that you connected 30 scanners with one account.
Scott
@ScottHaileRobertson
Has anyone had issues with Yarra slowing down scanners? Our engineering team suspects that when Yarra temporarily copies data to disk, the drive gets fragmented over time. We've had to do several load from colds on a few of our systems. It could be entirely unrelated to Yarra, but I just wanted to ask the group in case others have had this issue?? For reference we are backing up abut 20 GB of TWIX data per week.
Tobias Block
@tblock79
@ScottHaileRobertson Hi Scott, Would be good to get feedback also from other users, but we haven't experienced problems like that. We've been using Yarra for 10 years now (on ~ 30 scanners), and we are exporting crazy amounts of raw data every night. Even if the C: drive would get fragmented, I don't think that it would have a noticeable impact on the scanner performance because limited data is read from/written to the C: drive during normal scanner operation (the images, DB, and raw data are stored on other drives/computers). How exactly do you notice the scanner slow down?
Scott
@ScottHaileRobertson
The UI gets extremely sluggish (registering patients takes minutes for example). Rebooting helps somewhat, but our engineering team has been having to perform load from colds every few months to reset the systems. We have tons of WIPS and other things installed, so I don't think its Yarra either, but since its newest change to the system, its been the first thing to get blamed.
Tobias Block
@tblock79
An easy test would then be to see if the UI gets fast again when Yarra is not running. Thus, you could terminate RDS (via right-click on the Yarra icon), rename the installation folder, and reboot. If the UI remains slow after that, it is unrelated to Yarra (which I am sure it is). Also, disk fragmentation should not slow down the UI in such a way. There must be something else going on, I assume.
Dan Ma
@madan6711
@tblock79 Hi Tobias, I'm planning to install the RDS client on our vida system (XA20A). I see on the webpage that I will need a certificate to install the software. Can I get the certificate to use it ? Thanks !!
2 replies
Dario Bosch
@dabosch

Hi @tblock79 and others,

we're now having problems with RDS when we record large data files (>100GB). Unfortunately the C:-drive with the queue directory does not have a lot of free space, so those files >100GB cannot be exported via the queue.
What is your strategy to handle large files?

I've been thinking about a direct export feature, as discussed a couple of years ago. Basically having a parameter in rds.ini that would skip the queue and directly write the files to the network drive.

What do you think? Would you be willing to implement this? Or would you accept a patch into the official codebase?

4 replies
huchengMRI
@huchengMRI
@tblock79 Hi Tobias, we want to export image data in real time to a mapped network drive. We used to do it via IdeaCmdTool in VE11C. Now we have trouble doing it after upgrading to XA30. We can only export the data to a local drive but not a network drive for perhaps security reasons. I wonder if Yarra can help us with that.
Thanks.
Tobias Block
@tblock79
@huchengMRI Hi! Yarra does not support real-time export of the k-space data (i.e., while the scan is running). Data can only be exported once scanning has finished. The export can be triggered via the start menu (e.g., before taking the patient out of the scanner). Depending on the size of the scan, the data export can take a moment. Thus, it might be necessary to include some time for the data export in the scan slot/schedule. You can also export the data automatically at night. However, there is no guarantee that the data is still on the scanner's RAID filesystem at that time point. Thus, for very important data, I'd recommend to export it directly after the scan.
Walter Zhao
@walzhao99
Image from iOS (1).jpg
Hello, I am trying to install the RDS client on our Vida system (XA31A), but am not able to launch the client even after installing the XA certificates. Is there some way to troubleshoot the DeviceGuard CI policy? Shown here is the Windows Defender notification.
Tobias Block
@tblock79
@walzhao99 Hi Walter, Yeah, this problem has occurred here as well. It's related to a change of the Windows security policies that Siemens has introduced with the XA31A Service Pack 1 version. They have provided us with a way to change these settings again. I will send you these instructions in a private message (not sure if I am allowed to share publicly).
salmon38
@salmon38
Hi @tblock79, we are on VE11E and we're running the RDS client from an external hard drive (due to space constraints preventing temp storage of the files on the internal hard drive). Unfortunately it seems that RDS.exe won't start automatically when the scanner is booted due to the security features on this software version (we have to enable Update mode via the embedded control gui in order to launch the client). Have you or others found any workaround for this?
Tobias Block
@tblock79
@salmon38 Unfortunately, we don't have any experience with running Yarra from a USB drive. Maybe someone else here has? But it's wouldn't surprise me if the MREmbeddedControl system causes trouble in that case. Guess we should add the option to store the exported files in a different path (at least, for RDS), so that the Yarra executables could still reside on the C: drive.
moloney
@moloney
Hi, who do I contact for RDS certificates for XA30? We are migrating to this newer software versions soon and thus are looking for alternatives to our home grown Python script for transfering K-space.
Tobias Block
@tblock79
@moloney Please send me your email address in a private message and I will send you the certificates & instructions
Tobias Block
@tblock79
@salmon38 We added the option to buffer the exported files on a different location / drive than the Yarra binaries. It has been implemented, I just need to do some more testing and then will release a new version
1 reply
moloney
@moloney
Is there a reason for buffering at all, rather than writing the files directly to the network drive? I just tested and was able to use RaidTool.exe to write directly to a network drive.
Tobias Block
@tblock79
@moloney The reason is that writing directly to a network drive fails frequently. It seems that neither the Twix nor RaidTool are protected against network package loss. We had lots of problems with that here.
moloney
@moloney
Interesting, is this specifically on newer systems (e.g. XA30)? We just switched to XA30 but have been running a k-space backup script on Prisma (VB -> VE software version I think) for many years that copies directly to a network drive without issues. Is it possible to provide a direct transfer option in RDS?
Tobias Block
@tblock79
@moloney It happened across different software versions. Happens with the TWIX tool too, especially when saving large files. It might be dependent on the network quality (in our case, there are probably firewalls and network switches/routers in-between), but the conclusion among our researchers was that saving the data directly on the network drive is just not reliable enough.
Alexander Fyrdahl
@fyrdahl
Is the certificate mentioned in the instructions just the "normal" developer certificate? In theory, could I sign the Yarra binaries with a Python script that traverses all files and calls signtool.exe?
Tobias Block
@tblock79

@fyrdahl Hi Alexander, Yes, you can sign the Yarra client with your own (IDEA) developer certificate using the signtool.exe. I am just using the following .bat batch file for that, but a Python script would do it as well:

signtool.exe sign /fd SHA256 /f [put path & name of the certificate here].pfx %1%

You need to make sure to sign all .exe files, as well as all the .dll files (including the ones in the subfolders, such as \platforms)

Judd Storrs
@jstorrs
I have a XA system that was upgraded to XA30 and Yarra had been previously setup by a colleague who has left. The newest client complains about domain names vs the server and it looks like the check had somehow just been disabled in the previous client that was installed (but that is not compatible with XA30). I'm just not sure what needs to match when I approach IT. Is there a command I can run on the yarra server and on the scanner to get output of what each are seeing? I know the IP addresses of each side, just not sure if nslookup shows what I need to be debugging or if there's something else I need to dig into.
Tobias Block
@tblock79
@jstorrs Hi Judd, The DNS check is only needed (and done) for the Yarra LogServer functions (clinical workflow monitoring). Is that what you are using Yarra for? To get this to work, the scanner must have DNS enabled, and it must have an entry in your local DNS server. Moreover, the MRI scanner and the LogServer must be in the same network domain. This is a security mechanism to prevent that data accidentally could get sent out of the hospital network (e.g., when the server address has been incorrectly configured).
Judd Storrs
@jstorrs
I didn't realize it only mattered for the logserver, but I am also working on getting the logserver to work for that scanner. I was wondering whether I just need to ensure that "nslookup" works on the client (which I think could be done with LMHOSTS etc) or whether it needs to also work on the server. I've requested DNS entries though so hopefully that works out.
Tobias Block
@tblock79
@jstorrs Yes, exacly. The DNS check only happens on the client side. It's just checking if the MRI scanner and the server are both known to the DNS server (by executing nslookup for both IP addresses on the MRI scanner). Moreover, it's verifying that both DNS names reported by the name server have the same network domain.
Vitali Telezki
@vtelezki:matrix.org
[m]
Hello, is it possible to send reconstruction tasks to yarraServer without explicitly using SAC/ORT client if one already has the raw data files available?
2 replies
kpelkola
@kpelkola
Hello! would it be possible to get a new certificate for our research MRI scanner that was just upgraded to XA30?
4 replies