hyunsoolee0503
@hyunsoolee0503
Oh I'm sorry. I just heard from my colleague that I don't need separate certificates for each scanner. So I have all I need. Thank you!
Tobias Block
@tblock79
@marjolein90 Hi Marjolein, I believe the physiodata is stored (or can be stored) in the Twix file. There is a thread in the IDEA Discussion board on that (the IDEA Discussion board is broken, but I can send you the thread as PM). So in this way, you should be able to get the physiodata with RDS.
marjolein90
@marjolein90
@tblock79 I would appreciate that, thanks!
usmanUCL
@usmanUCL
@tblock79 Hi! Few questions regarding Yarra: Can Yarra software be configured to select the date from which we want the raw data to be transferred from (in case we are not interested in data before that date)? 2) On VA11, when scanner is rebooted, once we leave Kiosk mode, will Yarra software be automatically started in background if it is pinned within the start up? Thanks
usmanUCL
@usmanUCL
3) When data is being transferred to remote drive, is it possible to stop it using 'Postpone Active Transfer', I tried it few times, but it continues to transfer raw data files (I was thinking only current file will be transferred and then it will stop)
usmanUCL
@usmanUCL
4) If we install the Yarra software onto a network drive and want to save to the same, would it be possible to avoid the second step of transferring data as it will be redundant
Thank you for your time in answering my queries
Usman (RBHT)
Tobias Block
@tblock79
@usmanUCL Hi Usman,
1) You can't specify a date but there is a file in the Yarra folder called lpfi.ini that contains the "last processed file id". Thus, you could open the Siemens TWIX tool and look at the file id from where you want the update to be done and write it into that file.
2) Yes, that's correct. Once it's leaving the kiosk mode, RDS will be started if it's contained in the Windows Startup folder.
3) Currently, it will continue the active transfer (scan) and then postpone any further transfers. We can look into adding a "hard stop" button for a future version.
4) That's not possible at the moment. Running the Yarra Client on a network share works as a workaround, but it's not the intended way of operating it as it will block the scanner for much longer. However, if this is important for your project, you could build a custom version of the Yarra Client and modify the transfer logic accordingly (shouldn't be too complicated)
usmanUCL
@usmanUCL
Hi Tobias, Thank you for your reply, I was trying to find lpfi.ini file inside the Yarra folder but couldn't locate it, is there a direct link to it where I can find it? Thanks again.
Tobias Block
@tblock79
@usmanUCL Hi Usman, The file is not part of the distribution but will be created/updated at the end of each update run. The content should be:
[LPFI]
FileID=1234
usmanUCL
@usmanUCL
Thanks, I am able to find LPFI file and it is working as you kindly guided after modification. I still have issues in automatic start of RDS.exe once I leave Kiosk mode after reboot of scanner although I have placed the short cut in the start up mode. I can see RDS.exe under start menu of Task Manager but it doesn't start automatically. May be this is due to being on network drive rather than drive? Thanks again for your kind guidance.
usmanUCL
@usmanUCL
For modifying transfer logic so that it doesn't execute the second step of transferring (in case Yarra was installed onto network drive), which files need to be modified in the source code?
Tobias Block
@tblock79
@usmanUCL It could be that the security policies might prevent execution of binaries from network drives. A lot has changed in that regard in the recent Siemens software versions (I don't know too much about it, as I don't have access to MR scanners at the moment). You could check if it does work when starting it from the C:\ drive (in that case, it's likely due to security policies)
@usmanUCL The transfer logic is mostly defined in the file rds_processcontrol.cpp
Simon Warfield
@skwarfield
I would like to get the certificates to run Yarra on XA11
Tobias Block
@tblock79
@skwarfield Can you send me your email address in a PM? I will email you the certificates then
jennifersteeden
@jennifersteeden
Is the RDS case-sensitive?
Tobias Block
@tblock79
@jennifersteeden Do you mean case-sensitive regarding the tags that are written into the protocol name? Yes, the tags are evaluated case-sensitive
jennifersteeden
@jennifersteeden
Yes i did - sorry for not being more specific. Thank you very much for your swift response!
kkwst2
@kkwst2
Hello, hoping to get the software-specific compilation of the YarraLink sequences to send raw data from our Avanto MRI running VE11C to our Ubuntu workstation. Where would I forward the C2P?
Tobias Block
@tblock79
@kkwst2 We don't officially support the YarraLink sequence anymore (as we are not using it at our site). You can download the source code here:
http://yarraframework.com/addons/yarralink/
We haven't used it on VE11C (I believe the last version we used it for was VE11A) but it might compile for VE11C without many changes
kkwst2
@kkwst2
Thanks for the reply. The link give me an error "Cannot resolve the cset".
Tobias Block
@tblock79
@kkwst2 Thanks for pointing that out. Need to update the link. You can find the code here:
https://bitbucket.org/yarra-dev/yarralink/src/master/
hyunsoolee0503
@hyunsoolee0503
Hi Tobias, I have a question regarding the yarra RDS. Recently, there shows some errors like: -- ERROR: Available disk space too small for exporting data. I was just wondering how can I fix this error. It would be really helpful if you let me know where in the local drive I can check with and delete temporary files from.
Thanks,
Hyun-Soo
Tobias Block
@tblock79
@hyunsoolee0503 Hi! The Yarra Client requires disk space to export the raw data onto disk. It seems that you have not enough empty diskspace available to save the raw data. Yarra writes the files into a subfolder of the Yarra installation path. Check how much diskspace is still available on that drive (typically drive C:). Temporary files can be deleted, e.g., from C:\temp
hyunsoolee0503
@hyunsoolee0503
Thanks Tobias! I'll check the subforder of the yarra installation path and C:\temp. I really appreciate your support.
Solenn Toupin
@SolennToupin_twitter
Hi!! Yarra is working pretty good on our Aera VE11C system. We copied the .exe shortcut in Windows startup folder so that it starts automatically when we turn on the scanner every morning. The only issue is it won't start automatically every monday morning. We don't see anything that controls that in the settings. Do you have an idea of what could create that? Thks for your help!!
Tobias Block
@tblock79
@SolennToupin_twitter Hi! Yes, for some reason, programs don't start reliable via the Windows startup folder on VE11C. We have noticed that too. I would recommend adding the RDS command to the end of the batch file C:\Medcom\MriProduct\Inst\MROrdinaryUser.bat. This has worked reliably in our case. Make sure to set the MREmbeddedControlUI tool to UPDATE mode before editing the file
Simon Warfield
@SimonWarfield_twitter
Yarra pulls the raw data to the local drive, and then transfers it to the windows share. Does it then remove the raw data from the local drive, or does raw data accumulate in the local drive ?
Tobias Block
@tblock79
@SimonWarfield_twitter Hi! When the file has been transferred to the network share (or destination folder) the file will be removed from the local drive. It does not accumulate on the local drive
Johannes Töger
@johannestoger
@tblock79 I would like to try Yarra on our NX system. Could you please send the required certificates? Best, Johannes
Tobias Block
@tblock79
@johannestoger Hi Johannes, Just sent you the certificates via email.
ICUH
@ICUH
@tblock79 Hi Tobias. Is it possible to change the temporary file location for RDS to other drive? We are hoping to use external hard drive as temporary file location since c drive is getting almost full all the time and file transfer is terminated. Thanks
Tobias Block
@tblock79
@ICUH Hi! Yarra will save the temporary files in a subfolder of its installation path. So you could just install Yarra directly on the external hard drive and then it should buffer the files there
Christof Karmonik
@CKarmonik_twitter
I would like to use Yarra on a XA20/Vida. Could you please send me the required certificates? Thank you!
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?
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