XNAT 1.7.6 - Ultrasound upload through Compressed Uploader

[Chris Smith]

Good day all, 

We are in the final stages of testing for one of my projects and have run into a couple of issues with the uploading of the ZIP files.  We are uploading 1 subject at a time, and all the files are ultrasounds (using the OHIF plugin).  To make it easier for the end users we have set up the project to upload directly to the Archive. 

1) When the file successfully uploads, the link shows "UNKNOWN successfully added" but the anonymized name shows up.  Is this something I need to worry about?

2) The first ZIP file uploads without issue but any subsequent ones gives us an error "The process could not be completed due to exceptions - Session processing may already be in progress: AutoRun.  Concurrent modification is discouraged".  I'm getting this message even if it's 6 - 8 hours after the first file is uploaded. 

What am I doing wrong? 

Chris

[Moore, Charlie]

Hi Chris,

I'm having trouble following quite what you mean with number (1). Could you upload a screenshot without any sensitive information showing this?

For number (2), I would guess that there's two issues going on. First, have you installed the pipeline engine? If you don't have the pipeline engine installed, XNAT can't run AutoRun (a pipeline triggered whenever a study is archived), so the AutoRun pipeline will just stay "Queued" on the session in XNAT indefinitely. However, this should only be relevant if there's some type of merge going on, which could be indicative of either or both of these scenarios:

1. When you say you're uploading "1 subject at a time", does each subject only have one study [session]? If not, the compressed uploader really only supports a single study/session​ at a time.
2. Are you familiar with how XNAT assigns labels to DICOM studies? By default, XNAT will often try to use (0010,0020) Patient ID as the label for the session. The labels need to be unique within a project. That's defined here: https://wiki.xnat.org/documentation/how-to-use-xnat/image-session-upload-methods-in-xnat/how-xnat-scans-dicom-to-map-to-project-subject-session . New in XNAT 1.8, you can customize which DICOM elements are used for assigning the labels, so you can pick something more appropriate for your data. Coincidentally, XNAT 1.8 also mostly removes the need for the pipeline engine to be installed, so the AutoRun thing should go away.

Thanks,

Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Chris Smith <zlibra...@gmail.com>
Sent: Tuesday, March 16, 2021 10:40 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] XNAT 1.7.6 - Ultrasound upload through Compressed Uploader

 

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[Chris Smith]

Hi Charlie,

I've been trying off and on all day but now when I try and upload a ZIP XNAT hangs at 98%.  I've rebooted the server etc. so will try again later this evening.  

1. When you say you're uploading "1 subject at a time", does each subject only have one study [session]? If not, the compressed uploader really only supports a single study/session​ at a time. 

I'm uploading all the ultrasounds that were done at the same time, so I'm assuming this is a single study.

2. Are you familiar with how XNAT assigns labels to DICOM studies? By default, XNAT will often try to use (0010,0020) Patient ID as the label for the session. The labels need to be unique within a project. That's defined here: https://wiki.xnat.org/documentation/how-to-use-xnat/image-session-upload-methods-in-xnat/how-xnat-scans-dicom-to-map-to-project-subject-session . 

I'll take a look at the documentation; appreciate the link (I'm sure I've read it but I'll go through it again).  

I'll see if i can get 1.8 as that sounds like it'll make life a lot easier for me.  Thanks for your time!

Chris

I'lll 

[Moore, Charlie]

Hi Chris,

Are you using Chrome? There's an issue with the Compressed Uploader in 1.7.6 if you're using Chrome: https://issues.xnat.org/browse/XNAT-6403 . As a workaround, another browser should be fine, or upgrading to 1.8 should also fix this.

Thanks,

Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Chris Smith <zlibra...@gmail.com>

Sent: Tuesday, March 16, 2021 2:16 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] XNAT 1.7.6 - Ultrasound upload through Compressed Uploader

 

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[Chris Smith]

...I am using Chrome.  I'll try Edge (or upgrade...)....Thanks!

[Chris Smith]

Yay!  Once i switched to Edge the Upload works for the first file (still getting AutoRun message for the second, but I'm working on that next...).  Whew, that was simple.  

Here are the images showing the Unknown that I'm seeing.  Everything works - the images are viewable, the information is all correct etc. - I just am worried the Unknown is either something important or will cause problems later. Is there a way the User can specify the name when uploading (rather than by something in the metadata)?

[Moore, Charlie]

Hi Chris,

Right, here "UNKNOWN" is what XNAT is extracting as a session label. The likely cause of that is DICOM element (0010,0020) Patient ID being the string "UNKNOWN". The problem is that if you upload another session with the same "UNKNOWN" id, XNAT is going to try to put the data in the same session. If you want the session label to be user-specified instead of pulled from the metadata, the Compressed Uploader directly into the archive won't work. The main options for that would be:

1. The XNAT Desktop Client supports this (available here: https://download.xnat.org/)
2. You can script the upload with the REST API and specify whatever label you want there.
3. In the Compressed Uploader (what you're currently using), you can select "Prearchive" instead of "Archive", and then change the session label when archiving from the prearchive.

Thanks,
Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Chris Smith <zlibra...@gmail.com>

Sent: Tuesday, March 16, 2021 2:41 PM

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[Chris Smith]

Thanks Charlie - I got the Pipeline Engine installed and no longer seeing the message.  I'll follow up with the study team how they want to proceed Re: Naming.

Appreciate your time and hope you have a great afternoon.
Chris

[Chris Smith]

Good morning Charlie and all, 

I'm not sure what's happening now - the Pipeline Engine worked for a day, but now we're back to getting the "Session processing may already be in progress: AutoRun. Concurrent modification is discouraged." error.  Does the Pipeline Engine need to be configured or somehow setup within XNAT itself?  I didn't see any instructions in the documentation and have gone through everything I can see in the application and don't see anything.  I do see that the Pipelines page shows "No pipelines have been setup" - do I need to do something there?

Appreciate your time

Chris

[Moore, Charlie]

Hi Chris,

Might it be a timing issue? The AutoRun pipeline is fairly quick, but if XNAT attempts to merge into a session with AutoRun still running, that triggers that error. Either way, there being any type of merge going on here at all is problematic. I think the main thing to fix here is still the session label uniqueness issue, as that makes the AutoRun issue irrelevant.

Thanks,
Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Chris Smith <zlibra...@gmail.com>

Sent: Tuesday, March 23, 2021 5:55 AM
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[Chris Smith]

Thanks Charlie, so it's back to the Pre-archive and manually naming the Session then if I understood your previous email?

Chris

[Moore, Charlie]

Hi Chris,

I think that's one solution that would work. There's also still the desktop client and automated REST uploading. If upgrading to 1.8 is an option, using the new customizable routing feature where you can set which tag to pull the session label from is probably the cleanest option. That feature should affect the compressed uploader so it wouldn't require any changes to the workflow here.

Thanks,
Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Chris Smith <zlibra...@gmail.com>

Sent: Tuesday, March 23, 2021 10:00 AM

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