This project forked from pyushkevich/itksnap
ITK-SNAP medical image segmentation tool
Home Page: https://sourceforge.net/p/itk-snap/src/ci/master/tree/
License: GNU General Public License v3.0
For Radiological Convention, patient is lying supine (face up) in a hospital bed, and you are standing at the foot of the bed like doctors in the old TV shows with the paper charts.
Currently Radiological Convention in snap Preference Dialog is showing Axial from top of the patient, which is incorrect.
In the Axial view, patient's nose should pointing upward.
Issue only appeared for one c3d generated 4d image using -tile command, and only appeared when dropping image loading.
Todo:
-tile
Re-implement deformation grid for 3d and 2d warp images.
Currently snap only support 3d warp image. Add support for 2d warp image so that when choosing deformation grid mode for displaying 2d vector image, the deformation grid will show up.
Currently time point nickname only used for identifying time points in the workspace file. We need to add it to the slice views for time point identification in UI.
Original Issue Link: pyushkevich#28
Add Orientation Code, e.g. RAS, LPS to the header of the mesh file exported by ITK-SNAP.
Changing rendering parameters in the preferences used to trigger an update (or enable the button if continuous updates were off). That no longer happens, I have to change the segmentation image to get the update back
Same happens if I select "clear 3D display", update remains grayed out
Reorient Image from LPS to LPI changed relative position between labels. Currently the dicom reader reorients Echo Cartesian Dicom from LPI to LPS, but it creates a mirror image with flipped A-P direction. We need to change the reorientation target to LAS so the A-P direction is not flipped.
Change reorientation from LPI to LAS instead of LPS.
When executing from outside of the binary folder, itksnap-wt crashed with missing QT library error.
Orignal Post: https://groups.google.com/g/itksnap-users/c/Ndg7UfpVq_U/m/JIF7ZBEeAAAJ?utm_medium=email&utm_source=footer
Pre-vtk9 logic:
GenericSliceRenderer::Texture *
GenericSliceRenderer
::GetTextureForLayer(ImageWrapperBase *layer)
{
const char *user_data_ids[] = {
"OpenGLTexture[0]",
"OpenGLTexture[1]",
"OpenGLTexture[2]"
};
const char *user_data_id = user_data_ids[m_Model->GetId()];
// If layer uninitialized, return NULL
if(!layer->IsInitialized())
return NULL;
// Retrieve the texture
SmartPtr<Texture> tex = static_cast<Texture *>(layer->GetUserData(user_data_id));
// Get the image that should be associated with the texture
Texture::ImageType *slice = layer->GetDisplaySlice(m_Model->GetId()).GetPointer();
// If the texture does not exist - or if the image has changed for some reason, update it
if(!tex || tex->GetImage() != slice)
{
tex = Texture::New();
tex->SetDepth(4, GL_RGBA);
tex->SetImage(slice);
layer->SetUserData(user_data_id, tex.GetPointer());
}
// Configure the texture parameters
const GlobalDisplaySettings *gds = m_Model->GetParentUI()->GetGlobalDisplaySettings();
GLint imode =
(gds->GetGreyInterpolationMode() == GlobalDisplaySettings::LINEAR)
? GL_LINEAR : GL_NEAREST;
tex->SetInterpolation(imode);
// Set the mip-mapping behaviour depending on whether the image wrapper is rendering
// in image space or in display space
tex->SetMipMapping(layer->IsSlicingOrthogonal());
return tex;
}Contrast control point stuck with the 16-bit image but ok with the 8-bit image.
After dropping, the mesh does not get immediately rendered
Hi, I’ve found an issue with the polygon tool where after a bunch of slices in a row of drawing complex polygons the polygon tool will start making a box of segmentation around the edge of the polygon, rather than following the polygon. I’m attaching her a photo of the polygon I drew (this was the 7th slice I had done in this window), and then when I do red over all it makes a red rectangle around the outer edges of the polygon. When I do clear over all with the inverse polygon, it clears everything in a rectangle on the outer edges of the polygon tool (but not everything outside the polygon). It stops if you do a smaller, less complex polygon tool. Typically if I quit ITK-Snap and restart it goes away, but I’ve had it happen multiple times.
I have not been able to consistently reproduce it either, but it is definitely a common issue I’ve had multiple times. I have been using version 4.0.0-alpha.4 on a Mac. That image is from a workspace, so I can send you the workspace here, but I’ve found it on multiple different images. It only happens after using the software for a while. Regarding the number of vertices, I have absolutely no idea - I’m using the continuous polygon tool and tracing with an apple pencil (as I mirror ITK-SNAP to an ipad), so its a lot of vertices.
Issue appeared on an Intel Mac with MacOS 12.6. Reproduced on multiple images.
Not yet reproduced on other machines
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