Overlay tool shows overlays at incorrect coordinates

[bingwing]

hi, guys, @swederik @medihack @simonmd @jpambrun , thanks for the excellent work.

When i use the cornerstone in cornerstoneWADOImageLoader, there a few dicoms file shown black.

the core js code in the html:

cornerstoneWADOImageLoader.external.cornerstone = cornerstone; var dicomelement = document.getElementById("dicomImage");

function loadAndViewImage(dicombase64data, arealocation) {
    var element = document.getElementById(arealocation);

    try {
        cornerstone.loadImage(dicombase64data).then(
            function(image) {
                var viewport = cornerstone.getDefaultViewportForImage(
                    element,
                    image
                );
                console.log(viewport)
                cornerstone.displayImage(element, image, viewport);
                if (loaded === false) {
                    cornerstoneTools.mouseInput.enable(dicomelement);
                    cornerstoneTools.mouseWheelInput.enable(dicomelement);
                    cornerstoneTools.pan.activate(dicomelement, 2); // pan is the default tool for middle mouse button
                    loaded = true;
                }
            },
            function(err) {
                alert(err);
            }
        );
    } catch (err) {
        alert(err);
    }
}

cornerstone.enable(dicomelement);

Dicom files special, or i miss something?

Hope you can reply this thread, thank you very much!

[swederik]

It looks like that may be pixel data stored in Overlay tags: See http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.9.2.html

There is an open PR on Cornerstone Tools to support this:

https://github.com/cornerstonejs/cornerstoneTools/pull/860

If those images truly contain PHI (I see something that looks like a patient name), please remove it. You can black it out with paint and upload it again.

[bingwing]

Thanks, already black the PHI i think and upload again, what do we call the chart looks like in the first pic. And how can i show it correctly? do we have demos deal with this? looked up all the issues and didn't find any similar one.

[georggrab]

I've seen this before. Can you delete MinPixelValue and MaxPixelValue tags from your dicom file and try again? Alternatively, turning off strict mode in the WADO image loader config

[jpambrun]

@swederik assessment is correct. The first sample is likely a black image with a G6000 overlay. This is supported by the WL=1, WW=1 in the working viewer. In addition, the beige color overlay would otherwise be impossible on the grayscale MONOCHROME2 MR.

[bingwing]

Thanks, but i'm very new with dicom, is there a demo code or any reference could help me to solve this? @dannyrb @swederik @jpambrun

[bingwing]

I can see there provide overlayPlaneModule to parse overlay data.But the overlaydisplayTool seems to be have pending for a while here already. @dannyrb @swederik @kofifus @jpambrun , i was stucked deeply, is there any one could give me some advances? Thanks !

[kofifus]

I don't know why the overly tool is not merged, as far as I know there are no pending issues with it .. @dannyrb ?

[dannyrb]

@kofifus, I need to update that PR to not publish as a scoped package, and then it will be good for merge.

[bingwing]

Thanks! Very happy to hear this !! BTW, will it take long to do the merge , or where can i find a demo example code to experience in advance? @kofifus @dannyrb

[bingwing]

@kofifus @dannyrb Hint a issue when test the overlay tool, seems the overlays not get the right location as below pic shown.

Repro steps:

1. check out feature/overlay-tool and compile to get the .js package
2. import overlay tool to my project with code as other tool did like this: cornerstoneTools.init({ globalToolSyncEnabled: true }); const OverlayTool = cornerstoneTools.OverlayTool; cornerstoneTools.addTool(OverlayTool); cornerstoneTools.setToolEnabled("Overlay", {});

Did i miss something, hope someone could reply this thread. Thank you very much!

[dannyrb]

@bingwing if you can provide a minimal reproduction (repo or codesanbox), or anonymized files for testing, I would be able to take a closer look.

[bingwing]

@dannyrb @kofifus Sorry i can't find any anonymized files for sharing now, but after fork your codesanbox and testing[only the dicom file changed!], it also shown incorrectly. Screenshot as below.

should be like this

Thanks !

[bingwing]

@dannyrb @kofifus Problem solved !!!

After debugging feature/overlay-tool, i wonder that, is the code in line 100 odd ?

The setTransform executed twice, after delete line 100, everything becomes good.

Thank you for the excellent work again! Bing

[dannyrb]

@bingwing, thanks for the update! I'll shift this over to the tools repository and mark it as a bug report. Hoping to find some time here soon to merge the overlay tool. If you were able to provide example DICOMs to build a test case, that would be helpful 👍

[kofifus]

@bingwing - pls see this to explain why the transform is set twice https://github.com/cornerstonejs/cornerstoneTools/issues/780#issuecomment-476975576

perhaps @jdnarvaez can help here ?