How to adjust the distorted image?

Support
1

Hi!
After the data was loaded into 3D Slicer,the axinal and coronal view display normally,but the saggital view was distored.
I cannot understand the reason about this problem,furthermore,whether it is possible the problem happened to axinal or

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coronal view and how to adjust the distorted image?
Thanks!

2

Was the volume acquired with tilted gantry?

3

Sorry, I don’t know.The data of DICOM format was acquired through PACS (Picture archiving and communication system) and I have never met this problem before. So I consult with image doctor of our hospital, he have no idea about this too. The 3D Slicer is so powerful, so I think this problem could be solved with “reform” or “transform” module, but the result is failed.

4

We should be able to address this in Slicer, but we need some more information.

Install the latest nightly version of Slicer and follow these steps to collect the necessary information:

  1. Open the DICOM popup
  2. Select the CT image
  3. Click Metadata button
  4. Enter tilt in the search box
  5. Click Copy metadata button
  6. Paste the gantry tilt value in your response message here

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1 Like
5

The value of gantry tilt is 20.9,what should i do next?

6

We are working on a solution, probably will be ready in 1-2 weeks. You can monitor the status here: https://issues.slicer.org/view.php?id=4409

If you need a solution now then you can use a DICOM converter that supports gantry-tilted images, for example dicomtonifti. Download from here: https://github.com/dgobbi/vtk-dicom/releases

7

Thank you very very much,professor lassoan!

8

I implemented a fix that should work for the gantry tilt data, but I don’t have a sharable dataset for testing.

I’ll try to acquire images of a phantom but if anyone has data they can share that would save the trouble.

For the record on discussion with colleagues we determined that a good phantom dataset for testing would include:

  • a phantom with clearly marked up/down/left/right/front/back
  • data acquired prone and supine
  • slices acquired head first and foot first
  • data acquired with gantry tilt
  • data acquired with skips and/or variable table speed
  • use of different reconstructions (e.g. spiral data at 3mm and the same data at 5mm)
  • saved raw data for later reconstruction as needed

If I’m able to time on a scanner and help from a tech I’ll try to acquire these and make them public on midas.

9

Hello Steve,I have the distorted image in dicom format.But how can I share the data with you?

10

Hi doc-xie -

@lassoan was able to share some sample data with me for testing so after a few tweaks yesterday the new code linked above appears to be working. It will be good for you to test it too with your data once we get it into a build of the application, which should be available in a day or two.

Best,
Steve

11

Thanks Steve!
I will be keeping eyes on your achievements all the time,the problem has confused me for a long time.
Good luck!
doc-xie!

12

Thanks for the encouragement! :smile: Yes, I’ve been wanting to fix gantry tilted volume handling in Slicer for a long time too.

Since the the code is still new and relatively untested, @lassoan, @jcfr and I decided not to include it in the 4.8 release but will put it in the Nightly build after the release builds are made.

Best,
Steve

13

The pull request was merged today so it should show up in Nightly builds tomorrow. Would be good to know if it works for your data @doc-xie. Have a great weekend :sunny:

14

Good job!Thanks you very much,Steve!
Would you like tell the the details about the steps?In other words,what should I do after I setup the new Nightly builds or is there any extentions should be downloaded?
Best wishes!
doc-xie

15

Hi doc-xie -

No special steps should be required, just importing into the DICOM module and then if there’s a gantry tilt detected the loaded volume will be put inside of a grid transform that straightens it out. Of course I’ve only tried this with a few datasets so let us know how it goes for you.

Best,
Steve

16

Ok!Steve:smile:
Another question,if the data is in .nii format,how to adjust the distorted image?
Thanks!

17

Ah, sorry, the solution I implemented only work with DICOM because that’s where the original image geometry information is available. I’m not sure there is a good solution for nii files unless you know the gantry tilt angle and can manually construct a shear matrix to correct it.

-Steve

18

Thanks for your quick answer!
But where can I find the gantry tilt in the menu?Is it in the Metadata,and I shoul search it with word"tilt" ?
Best,
doc-xie!

19

image
The value of the gantry tilt has not been shown in the interface!

20

This is the original image of the volume
image