Sending data to XNAT from OsiriX?

[Tyler Ketchabaw]

Hi all,

We've built an XNAT instance for our lab and are trying to integrate it into data acquisition as well as data storage, i.e. getting the data transferred from the scanner to XNAT. Our Radiology department uses a GE scanner and due to GE firewall restrictions, they are not keen on sending us the data directly from the scanner. Rather, they push the data from the scanner to one of two Macs running OsiriX, and then they burn the data to CDs from there and distribute the disks to investigators as needed.

Obviously, it would be nice to cut out that last step, and if they insist on not using the scanner's DICOM server then OsiriX is our next best bet since it's already set up. After trying (unsuccessfully) to send data to our XNAT's C-STORE SCP, I did some further googling and found that XNAT Gateway might be necessary as a mediator between XNAT and OsiriX; however, it was not immediately clear to me if it would be possible to upload data from OsiriX to XNAT. It seems like it is meant more for configuring OsiriX to look at images from XNAT.

Can anyone comment?

Thanks

Tyler

[Daniel Marcus]

Hi Tyler,

That's exactly right -- XNAT Gateway is intended to pull DICOM from XNAT into Osirix (or any other DICOM workstation or modality).  It is needed b/c the DICOM network protocol itself is not secure (no encryption or user access control) and so Gateway adds a security layer.

For getting data from Osirix to XNAT... it seems like the C-STORE operation from Osirix to XNAT should work. It may just take some noodling around.  Quite possibly there are network firewall issues related to the DICOM ports.   Perhaps you could post the errors you're seeing.  

Also, if you want to automate things a bit, I wonder if you could setup CTP on the Macs that are receiving the data.  From CTP, you could relay the files to both Osirix and XNAT's DICOM receiver.  Again, you'd need to work through the network issues, but it could be a nice automated workflow.  And it would give you SSL encryption that you don't get with direct DICOM sends.  CTP, by the way, is an RSNA product that we use frequently in conjunction with XNAT for just this sort of thing.

http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor

https://wiki.xnat.org/display/Workshop2012Pub/XNAT+Workshop+2012+-+Data+Upload+and+Entry

-Dan

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[Herrick, Rick]

That’s interesting. I’ve used OsiriX frequently in the past to send images to XNAT and never had a problem… Until just now. What’s weird is that it’s not all images: some work, some don’t.  All of the images that fail to send properly from OsiriX seem to send with no problems from DicomBrowser. It’s not related to size: I just sent an 11GB study from OsiriX to my XNAT dev instance as well as a 16MB X-ray of my dog’s injured leg (it wasn’t broken, just a little ligament damage: he’s fine now).

I kinda feel like it’s something on the OsiriX side because I’m not seeing anything at all happening on the XNAT side, but it’s possible that I’m not looking in the correct place.

I’ve filed a bug on this (https://issues.xnat.org/browse/XNAT-3590) and we'll look into it.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

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[Herrick, Rick]

Oh, one thing I wanted to add. You may want to try changing the transfer syntax to Implicit Little Endian and see if that makes a difference. You can change the location definition within OsiriX so that it defaults to Implicit Little Endian by default, but you can also test this just by changing the transfer syntax in the Send dialog:

I’ve had that make a difference in the past, although it’s not fixing the studies that aren’t sending now…

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

[Tyler Ketchabaw]

Hi Rick,

Thanks for filing a bug on this. I'm just following up now to see if there's been any progress made on this, since the link says it hasn't been assigned to anyone yet. We've got ~150-200 scans coming our way in the coming months so it would be super helpful if we can get this straightened out soon.

Thanks!
Tyler

[Yash]

Hi Tyler, 
were you able to use Osirix to upload data to XNAT?

It would be of great help if you can share how you did that. As mentioned in your question i followed all the steps on XNAT wiki, but wasn't able to install Gateway_Gui.app on my mac, which is required for connecting to XNAT server. 

Any pointers will be helpful.

Thank you!

Yash

[Herrick, Rick]

I was just able to take a PET/MR session and send it from OsiriX 7.0.1 64-bit running on OS X 10.11.3 to an XNAT 1.6.5 server. The data arrived in the prearchive properly and archived with no issues. I was also able to send the X-ray of my dog’s leg that had previously failed and everything worked fine there.

You mention having trouble installing the gateway application. That is only required if you’re sending over a long-haul connection. If you’re located close to the XNAT instance, you shouldn’t need that. XNAT has its own DICOM SCP receiver, which has the AE title XNAT and port 8104 by default (you can change this by modifying the file dicom-import-context.xml in your web app’s WEB-INF/conf folder and restarting Tomcat). The only other info you’ll need is the server address. This is my OsiriX configuration for the server to which I just sent data successfully:

I suspect the problems from last year were caused by a particular version of OsiriX. Like I said, I had been able to send from the application previously and I am able to send now, so those failures were 99% likely to be an OsiriX issue.

If you are sending a long-haul connection, e.g. outside of your institute or university firewall, then you would probably need the gateway. If you’re having trouble setting up the application and OsiriX to work together, have a look at this page:

https://wiki.xnat.org/display/XNAT/XNAT+Gateway+Setup+for+Osirix

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

Visit this group at https://groups.google.com/group/xnat_discussion.

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[suyash Bhogawar]

Thank you Rick!

Yes i have been refering to the link. As it says,  i will need XNAT gateway i downloaded it from here. the problem is gateway app doesn't get installed on my mac neither it shows any error. I think as i am not able to install gateway app on my mac, i am not able to connect my OSIRIX to XNAT. 

Thank you!

Yash

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[Herrick, Rick]

Where is the XNAT to which you’re sending data? Is it outside your firewall?

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

[Tyler Ketchabaw]

Hi guys,

I can confirm that our XNAT began cooperating with Osirix some time early this year. In a truly classic debugging session I decided to re-try the connection without changing any of the settings and it worked perfectly. We haven't had a problem since. Still not sure what the issue was but it's fixed now!

Tyler

[suyash Bhogawar]

It's inside the firewall. 

here is the error i am getting.

3/30/16 11:30:55.631 AM OsiriX Lite[16140]: DCMTKStoreSCU: _numberSent: 0 / _numberOfFiles : 56304

On Wed, Mar 30, 2016 at 10:22 AM, Herrick, Rick <jrhe...@wustl.edu> wrote:

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Where is the XNAT to which you’re sending data? Is it outside your firewall?

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961