image_applymask
Apply a binary mask to a 3D or 4D image.
Keywords : Image, Mask, BET
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(image), path(mask)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| image | file | 3D or 4D image to apply the mask to. | True | *.nii.gz |
| mask | file | Binary mask to apply to the image. | True | *.nii.gz |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*masked.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| *masked.nii.gz | file | Masked 3D or 4D image. | True | *masked.nii.gz |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| first_suffix | string | Suffix for the output image file. This will be used as the first part of the suffix, followed by “_masked”. | “ | |
| single_thread | boolean | If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task. | False | |
| data_type | string | Data type for the output image. Use the following format: uint8, int16, int32, int64, float16, float32 or float64. Original type is preserved if data_type is not supplied. | “ |
| Description | DOI | |
|---|---|---|
| MRtrix3 | MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging. | 10.1016/j.neuroimage.2019.116137 |
Authors
Section titled “Authors”Last updated : 2026-09-24