registration_tractogram
Apply a transform to a tractogram or multiple tractograms. Supports .trk, .tck, and .h5 formats. Please note that removing single or overlapping points is only supported for .trk or .tck files.
Keywords : Diffusion MRI, Registration, Bundles, Tractogram
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(anat), path(affine), path(tractogram), path(reference), path(deformation)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| anat | file | FA nifti format as anatomical image | True | *.{nii,nii.gz} |
| affine | file | ANTs affine transform | True | *.mat |
| tractogram | file | Tractogram or list of tractograms to register | True | *.{trk,tck,h5} |
| reference | file | Reference anatomy for tck/vtk/fib/dpy file support (.nii or .nii.gz) (optional) | False | *.{tck,vtk,fib,dpy} |
| deformation | file | Path to the file containing a deformation field (optional) | False | *.{nii,nii.gz} |
Outputs
Section titled “Outputs”tractogram
Section titled “tractogram”Format : tuple val(meta), path(*.{trk,tck,h5})
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *.{trk,tck,h5} | file | Warped tractogram(s). | True | *.{trk,tck} |
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 | |
|---|---|---|---|---|
| inverse | boolean | If true, the affine transform will be inverted before being applied to the tractogram. | False | |
| reverse_operation | boolean | If true, applies affine and deformation in reverse order (deformation first). | False | |
| invalid_streamlines | string | How to manage invalid streamlines after applying the transform. Either ‘keep’ invalid streamlines in the tractogram, ‘cut’ invalid segments and keep the remainder or ‘remove’ invalid streamlines entierly. NOTE : selecting ‘keep’ disables overlapping and single-point streamlines detection. | cut | - keep - cut - remove |
| remove_single_point | boolean | If true, removes single-point streamlines after applying the transform. | False | |
| remove_overlapping_points | boolean | If true, remove streamlines with overlapping points after applying the transform. | False | |
| no_empty | boolean | Don’t save empty tractograms. | False | |
| threshold | float | Maximum distance between two points to be considered overlapping, in mm. | 0.001 |
| Description | DOI | |
|---|---|---|
| ANTs | perform registration using transform as input | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-12-22