Module: image/burnvoxels
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Burning Voxels: The module takes binary masks and “burns” or imprints their voxels onto an anatomical image. This means that the areas defined by the masks are marked or labeled on the anatomical image.
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Output Images: The module generates multiple output images:
- One image with all masks burned onto the anatomical image.
- Separate images for each mask burned onto the anatomical image. If there are N masks, there will be N images.
- Label Values: The burned voxels are assigned label values:
- The minimum label value is 25.
- Subsequent label values are incremented by a dynamically determined step based on the number of masks.
In summary, this module processes an anatomical image by applying binary masks to it, generating multiple labeled images as output.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| masks | list | List of binary masks to be burned onto the anatomical image. | *.nii.gz |
| anat | file | Anatomical image to burn the masks onto. | *.nii.gz |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| all_masks_burned | file | Anatomical image with all masks burned onto it. | *.nii.gz |
| each_mask_burned | list | Anatomical image with each mask burned onto it. | *.nii.gz |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| ANTs | Advanced Normalization Tools (ANTs) for image processing. | http://stnava.github.io/ANTs/ | |
| MRtrix3 | MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging. | https://www.mrtrix.org/ | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git |
Keywords
| Image Processing |
| Voxel Burning |
| Mask Application |
Authors
@GuillaumeTh
Maintainers
@GuillaumeTh