Odd "null" image problem

[Simon Doran]

Hi Kevin, Rick, et al.

  Have you ever seen DicomBrowser behave in the way seen in the attached image?

  All files corresponding to the "null" entries in this screenshot are present in the data source, in the same directory as the files that are read correctly. Moreover, the files all read correctly on other systems that we use for DICOM image analysis.

  Any ideas where we can look to try and debug this?

  Best wishes,

Simon

[Herrick, Rick]

What version of DicomBrowser are you using?

Could you possibly share the series that has both nulls and not nulls in it? Even a few frames of each would probably be sufficient.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

--
You received this message because you are subscribed to the Google Groups "DicomBrowser users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dicombrowser-us...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[Simon Doran]

Hi Rick,

  Thanks. My user is back in on Monday and will let me have the series then. What's the best way to share the files? I would say XNAT, but the whole problem is that DicomBrowser is my means of uploading the files to XNAT :-)

Simon

[Herrick, Rick]

If it’s just a few frames, you can just zip and email them.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

From: <dicombrow...@googlegroups.com> on behalf of Simon Doran <simon...@icr.ac.uk>
Reply-To: "dicombrow...@googlegroups.com" <dicombrow...@googlegroups.com>
Date: Friday, January 8, 2016 at 4:51 AM
To: DicomBrowser users <dicombrow...@googlegroups.com>

--

You received this message because you are subscribed to the Google Groups "DicomBrowser users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dicombrowser-us...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Simon Doran]

Hi Rick,

  It's easiest to give you access to the whole study. You can pick it up from here:

https://lft.icr.ac.uk/www/?a=d&i=7629509123

  Study 14 is the one where the nulls and correctly read files are mixed. All studies after 14 seem to be null.

Simon

On Friday, 8 January 2016 17:08:11 UTC, Rick Herrick wrote:

If it’s just a few frames, you can just zip and email them.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

From: <dicombrow...@googlegroups.com> on behalf of Simon Doran <simon...@icr.ac.uk>
Reply-To: "dicombrow...@googlegroups.com" <dicombrow...@googlegroups.com>
Date: Friday, January 8, 2016 at 4:51 AM
To: DicomBrowser users <dicombrow...@googlegroups.com>
Subject: Re: Odd "null" image problem

Hi Rick,

  Thanks. My user is back in on Monday and will let me have the series then. What's the best way to share the files? I would say XNAT, but the whole problem is that DicomBrowser is my means of uploading the files to XNAT :-)

Simon

 

[Simon Doran]

P.S. Version is 1.5.2.

[Herrick, Rick]

I’m not seeing this at all:

That’s with 1.7.0b4 on OS X.

What occurred to me when I looked at this again is that that what’s missing there is… very weird. I mean, it’s missing the file name. Not the metadata or anything about the actual DICOM, but the file name, which shouldn’t be a problem what with the fact that it looks like it’s actually opened the file. Would it be possible for your user to upgrade to the latest 1.7 build up on the FTP site and see what happens?

--

You received this message because you are subscribed to the Google Groups "DicomBrowser users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dicombrowser-us...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Simon Doran]

Curiouser and curiouser!

I just downloaded the images as a zip file from the same lft.icr.ac.uk link as you just did.

Are there any logs I can look at? Could our two versions somehow be picking up different libraries, since I do also have DicomBrowser1.5.2 installed on the same machine?

Simon

[Kevin Archie]

Also probably a good idea to compare JVM versions.

  - k

--
You received this message because you are subscribed to the Google Groups "DicomBrowser users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dicombrowser-us...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

<DicomBrowser_problem.png>

[Simon Doran]

Thanks, Kevin.

I have multiple versions on my system. How do I tell which one DicomBrowser is actually running under?

Simon

[Herrick, Rick]

The best way that I can see to do it is to go into Activity Monitor, find the DicomBrowser process, double-click on it to open the page for that process, then look at the Open Files and Ports tab. If you take all of those files (you should probably delete all of the references to fonts: there’s a lot of them and they won’t tell you anything useful), you will probably find something like /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM (the “A” path may differ, but what you’re really interested in is what Current, at the same level in the folder, is symlinked to: in my case Current is symlinked to A).

Under there, you’ll find a folder named named Commands. That’s the equivalent of the bin folder in a standard JVM distribution. That means you can run this:

$ /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java -version

java version "1.8.0_60"

Java(TM) SE Runtime Environment (build 1.8.0_60-b27)

Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)

And that’s what I’ve got. I think that it will always use that same framework, so the short answer would just be to run that command up above.

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

From: <dicombrow...@googlegroups.com> on behalf of Simon Doran <simon...@icr.ac.uk>
Reply-To: "dicombrow...@googlegroups.com" <dicombrow...@googlegroups.com>
Date: Thursday, January 14, 2016 at 12:42 PM
To: DicomBrowser users <dicombrow...@googlegroups.com>
Subject: Re: Odd "null" image problem

--

You received this message because you are subscribed to the Google Groups "DicomBrowser users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dicombrowser-us...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.