jilei-hao / itksnap

ITK-SNAP medical image segmentation tool

ITK-SNAP README

Welcome!

Thank you for your interest in ITK-SNAP! By using this program you are joining an ever growing community of users from research labs around the world. ITK-SNAP is an open-source software application made possible by the committment of dedicated developers, who often make contributions on a volunteer basis. Original development of ITK-SNAP was supported by the U.S. National Library of Medicine through PO 467-MZ-202446-1. Subsequent development of ITK-SNAP version 2.0 has been supported by the U.S. National Institute of Biomedical Imaging and BioEngineering and the NIH Blueprint for Neuroscience through grant 1 R03 EB008200-01. Development of ITK-SNAP versions 3.0 - 3.6 has been supported by the NIH grant 1R01 EB014346.

ITK-SNAP is the result of over 15 years of work by many researchers, software engineers and students. Please visit the Credits page to learn about the team that made ITK-SNAP possible!

Please remember to cite ITK-SNAP

Citations in published work is the best way for us to gauge ITK-SNAP impact. As of the Fall of 2016, ITK-SNAP has been cited by over 2000 papers. If you use ITK-SNAP for a publication, please cite the paper below.

• Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage. 2006 Jul 1; 31(3):1116-28.

Getting Started

ITK-SNAP was designed for ease of use. There are several resources to get started with it.

• If you downloaded ITK-SNAP as a binary executable from itksnap.org, you can get started by reading the online tutorials.
• If you downloaded ITK-SNAP source code, please follow these online instructions to compile and build ITK-SNAP.
• You will need a 3D image to use this software. Images with which ITK-SNAP is known to work are found on the ITK-SNAP download page
• There are also materials (images, exercises, video) from training courses available on the documentation page.

Asking Questions

If you have a question about ITK-SNAP, here are the places where you may find an answer. Keep in mind that since ITK-SNAP in not a commercial product, it may take some time for an answer to arrive.

• If you have an question about how to use SNAP or why it's not doing what it should, post in on the ITK-SNAP Users' List.
• If you have a technical question or a questing related to ITK, join the ITK Users' Mailing List and post your question there.

Get Involved!

Your participation as a user, developer or sponsor is essential to ensuring a bright future for ITK-SNAP. There are many ways in which you can contribute to the stability and quality of this program:

• By participating in the ITK-SNAP User and Developer Mailing Lists.
• By reporting bugs and suggesting enhancements using the Bug Tracker.
• By joining the ITK-SNAP Development Team on SourceForge.net and contributing source code.

itksnap's Issues

Disable "how to display mesh layers" for Segmentation Mesh Layer

Mesh layer change does not change actor map content

Add dialog reminding the time point user is loading mesh into, and a "no further reminder" checkbox

Add minimum starting time to image loading progress bar

SNAP Assertion Failure in debug builds

Random white block rendered near the boarders of the viewports when resized

Issue appeared on an Intel Mac with MacOS 12.6. Reproduced on multiple images.
Not yet reproduced on other machines

Add hotkey for toggling 4D animation

Orientation inconsistency and typo in preference dialog and popup window

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.

Add Orientation Code to Mesh Export

Description

Add Orientation Code, e.g. RAS, LPS to the header of the mesh file exported by ITK-SNAP.

• Use main image orientation code
• Refer this doc for options and their formats: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/Slicer#Slicer_5.0:_Models_are_sav[…]ordinate_system_by_default
• Slicer Comment Embedding logic: https://github.com/Slicer/SlicerGitSVNArchive/blob/c0829f596f0ea661e0c5484056bd1374a3d22958/Libs/MRML/Core/vtkMRMLModelStorageNode.cxx#L421-L647

Questions

• Is SNAP converting everything to RAS orientation?
• Is mesh exporting converting everything to RAS?

Reset color legend when mesh is unloaded

Color Bar improvement

Requirement

• Enable color bar toggling
• Color bar match contrast settings

Echo Cartesian Dicom Reorientation fix

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.

Requirement

Change reorientation from LPI to LAS instead of LPS.

Mesh Loading Issues

Occasional Mesh File Dropping Failure

After dropping, the mesh does not get immediately rendered

Mesh dropped to current time point loaded to first time point

Contrast control point stuck for images with big intensity range

Contrast control point stuck with the 16-bit image but ok with the 8-bit image.

• The data types are the same. But 16-bit image's actual intensity range is bigger than the 8-bit image

MNI1528bit.nii.gz
MNI15216bit.nii.gz

itksnap-wt usage typo

Nickname issues in Layer Inspector for Segmentation Mesh

Description

• Distinguish Segmentation Image Mesh Layer with Image Layer with different displayed name in Layer Inspector Row
• Changing Segmentation Image Name not reflected in Segmentation Mesh Layer

Toggle for 3D Color Bar

Requirement

• Add a toggle in ViewPanel3D for the color bar display. Default to on for standalone meshes, off for label mesh.

itksnap-wt library linking error when executed from outside of the binary folder

When executing from outside of the binary folder, itksnap-wt crashed with missing QT library error.

Hide Label in 3D View not applied to all time points

Disable ColorMap for Segmentation Mesh, like colormap for segmentation image

Description

• Color Map panel should be entirely disabled for Segmentation Mesh, just like for Segmentation Image
• Bug: Program crashed when click on the disabled colormap panel

Enable 3D segmentation export from 4D segmentations

c3d tiled 4d image dropping caused seg fault

Issue only appeared for one c3d generated 4d image using -tile command, and only appeared when dropping image loading.
Todo:

• Test if any logic specific to image dropping caused the crash
• See if it related to c3d image generation using -tile

Preference change and "clear 3D display" does not enable "update" button for 3D view

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

timepoint change resets active mesh data array id

ITK-SNAP 4.0 Release Note

Mesh not render immediately after changing layer

Add Progress Bar for Dicom Series Loading

Reversed function for "Tiled" and "Thumbnail" buttons in the "Display Layout Inspector"

Segmentation Color Legend Issues

Multiple Color Legend Changes

• Title of the color legend does not change when switching from external mesh to seg mesh
• Label color legend display incorrectly when skipping certain numbers
• Separate label and non-label color legend visibility

When image loading failed, progress bar stays to hang entire program

Mesh Series Loading not started from current time point

Add STL Mesh Scene Export

Dicom series loading itk error in 4.0

004_COR_PD.zip

3D Cross Hair not respond to preference visibility change

Workspace loading error on image format

Display TimePoint nickname in the Slicing Views

Description

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.

Add Deformation Grid for 2D warp image

Description

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.

MINC Support

Original Issue Link: pyushkevich#28

Update splash screen information for 4.0 release

DEVWIN testing environment setup

Interpolation Mode Preference Issue in ITK-SNAP 4.0 Alpha-3

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;
}

Dr.Pressman Meeting Presentation

Deformation Grid not rendering for multicomponent images

Description

Re-implement deformation grid for 3d and 2d warp images.

Note

• Render a 2D vtk polydata together with slice rendering
• Use existing function to compute point coordinates
• Connect points with edges (celltype = line or vertices?)
• Change color by user preferences

Production Logic

https://github.com/pyushkevich/itksnap/blob/7a104c25401ce23599dc8d32ea80f3daae80f379/GUI/Renderer/GenericSliceRenderer.cxx#L604

Polygon tool paint incorrectly when tracing on an iPad mirror

Original User Report

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.

Wrong tp rendered when loading 4D seg to non-first tps

Closing additional image layer with volume rendering crashes the program

Use icons for (point data) and (cell data)

Layer inspector context menu improvements

Remove Mesh-unrelated items for mesh layer

Open/Close image for mesh layer should be Open/Close mesh

Vector mesh data improvements

Component 0 and Magnitude have same contrast

Hide/Disable Vector Mode for single component mesh data

nrrd file reading assertion error on Windows

• Tested OK on windows for release mode
• Was able to reproduce the issue in windows debug builds