ITKElastix

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Errors in elastix/parameter file lead to unclear error messages

2

I've just started experimenting with this package and ran into some start-up problems, mainly due to some unclear error messages. I was using parameter files that worked fine with base...

Svdvoort

itk.ParameterObject.New() This line of code takes 23 seconds to execute

2

The first time itk.ParameterObject.New() is executed take 23 seconds. Whether it can be accelerated

tianXinsha

Hello, I am trying to use itk elastix to estimate the deformation happened between two images (Suppose to be ultrasound images, but I am using some known deformation data to...

BH4DKC

ITK version 5.1.0 Python version 3.8.10 I'm trying to use SimpleITK on Python to do registration with histological images and mri images using this function ```python def get_image_from_elastix_with_masks(fixed, moving): elastixImageFilter...

Ambistic

As a follow-up / replacement for commented cells removed in #199 , create a dedicated notebook for napari visualization that additionally: - Uses the [itk-napari-conversion](https://github.com/InsightSoftwareConsortium/itk-napari-conversion) package to preserve metadata -...

thewtex

Replace checkerboard / compare functionality removed in #199 . Use pending improvements in 1.0aX by @PaulHax.

thewtex

Problem when opening a big TIF file

8

Hello, I am doing mouse brains alignement to the Allen Brain Atlas. Samples are optically cleared and images are obtained on a light sheet microscope. It works nicely on small...

Jeremie-BIC

Documentation and import fixing

6

Is there any documentation on the full API of ITKElastix? Although the examples are helpful, it can sometimes be hard to find exactly what modules/functions are available and what input...

Svdvoort

Feature: Write log to file without writing transform parameters

3

Currently, in order to write the log to file you need to do the following: ``` elastix_object = itk.ElastixRegistrationMethod[itk.Image[itk.F, 3], itk.Image[itk.F, 3]].New() elastix_object.SetLogToFile(True) elastix_object.SetLogFileName("out.log") elastix_object.SetOutputDirectory("/data/") ``` However, by using `elastix_object.SetOutputDirectory`,...

Svdvoort

Example notebook for reading / writing point sets from standard file formats

1

Depends on #75. Use `itk.meshread`, `itk.meshwrite` to read write `itk.PointSet`'s for registration.

thewtex