Connection (ImageXd)
Connection allows the mapping of fibres, planes or spherical structures. It creates a tensor field based on all voxels and its surroundings.
In this example, we use a part of an image stack from Julian Sartori (Thanks for the support!), which shows the achilles tendon of a rat.
Download: Image stack
To convert Dicom to the Nifti (nii) file format you can use dcm2niigui from Chris Rorden’s Neuropsychology Lab or 3DSlicer an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
First step
Load a image stack and show its content.
→ ImageXd
scalar.load stack.nii.gz scalar.info stack.nii.gz stack-info.txt scalar.analysis.image stack-analysis.png // more under the topic 'Histogram' scalar.setrange scalar.setcrop scalar.gradient stack-gradient.png // more under the topic 'View'
![]() scalar.analysis |
![]() scalar.gradient |
Second step
Calculate the tensor field.
→ ImageXd
scalar.use scalar scalar.load "stack.nii.gz" thread.max := 6 scalar.connection 16 //scalar.connection.x2 10 // tensor.center tensor.save "stack_tensor.nii.gz"
Third step
Evaluation (with 3DSlicer).
![]() stack_tensor.nii.gz (x,y view) |
![]() stack_tensor.nii.gz (y,z view) |
![]() stack_tensor.nii.gz (x,z view) |