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L-R mislabel in HTML viewer

Questions or comments about Mango, webMango, iMango or Papaya.

Moderator: Michael Martinez

L-R mislabel in HTML viewer

Postby dpat » Fri Mar 08, 2019 9:05 am

Hi,

We've been delighted by the HTML page export in mango, but just noticed that L and R are flipped in the output and mislabeled (so, a big lesion we know to be on the left, and which displays and is labeled correctly in mango, is labeled as being on the right in the HTML viewer!).

Thanks,

Dianne
dpat
 
Posts: 16
Joined: Wed May 26, 2010 3:47 pm

Re: L-R mislabel in HTML viewer

Postby admin » Sat Mar 09, 2019 3:41 pm

Are the original images DICOM or NIFTI? Can you take a screen capture of the "Create Webpage" screen so I can see what parameters you're using? If you possibly have an image that you can share with me that demonstrates the issue, that would also really help.

Also, do you use the "radiological display" option in Mango?

Thanks.
admin
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Joined: Fri Jul 06, 2007 8:18 am
Location: Research Imaging Center

Re: L-R mislabel in HTML viewer

Postby dpat » Sun Mar 24, 2019 3:02 pm

Hmm, mysterious. I am trying to reproduce the L-R error and it isn't happening.
I'm using NIFTI images. I tried both my work and home machines (Mac Pros Mojave),
and although one is set to radiological and the other is set to neurological display, both produce the correct output when I create the webpage.

I can only imagine that there was something wrong with the header of the original NIFTI file I had the problem with...but I cannot lay my hands on precisely that image (apparently)...though I found a T1 for the subject.

So, sorry, but I think there was some problem on my end, not yours. If I ever reproduce it, I'll let you know ; p

-Dianne
dpat
 
Posts: 16
Joined: Wed May 26, 2010 3:47 pm

Re: L-R mislabel in HTML viewer

Postby dpat » Tue Apr 16, 2019 3:57 pm

I have an example of the Left-Right switch problem:
You can download the nifti file here:
https://www.dropbox.com/s/5jqmngcgtzr7i ... ii.gz?dl=0
The image was acquired recently on our Siemens Skyra. It is a T1_mprage. It was converted from dicom using dcm2niix through Heudiconv. There is a large lesion of the left. Although I am providing the defaced version, I had the same problem with the non-defaced image.
I displayed the image in mango (where the stroke lesion is easily visible on the left). I chose "Create Webpage"->Create (no other options). The lesion is now on the right in the web browser (marked as anatomical right).
I'm using Mango 4.1: Preferences: Image Origin Default LAS, View Radiological.
I tried switching to Neurological, but get the same problem.

Thanks for your help.

-Dianne
dpat
 
Posts: 16
Joined: Wed May 26, 2010 3:47 pm

Re: L-R mislabel in HTML viewer

Postby dpat » Wed Apr 24, 2019 10:52 am

Please let me know if you have any problems downloading the sample image.

Thanks so much,

Dianne
dpat
 
Posts: 16
Joined: Wed May 26, 2010 3:47 pm

Re: L-R mislabel in HTML viewer

Postby admin » Sun May 05, 2019 4:12 pm

Thanks. I got the image and am able to recreate. Working on a fix. Will post here when it's ready.
admin
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Posts: 77
Joined: Fri Jul 06, 2007 8:18 am
Location: Research Imaging Center

Re: L-R mislabel in HTML viewer

Postby dpat » Thu May 09, 2019 1:53 pm

I just want to say that I finally understand the problem myself. AND, that I am also encountering it in imango.

If the header reports this for the sform or qform: *form_xorient Left-to-Right, then we get the problem in imango and papaya, but not mango.

Images that are fixed so that they report Right-to-Left seem to work correctly:
fslswapdim input -x y z output
fslorient -swaporient output

Thanks,

Dianne
dpat
 
Posts: 16
Joined: Wed May 26, 2010 3:47 pm


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