output_template_space
Subworkflow: output_template_space
This subworkflow is used to output files in a specific template space.
It leverages the templateflow template repository to fetch the requested
template and its associated files, then register the input files to the
requested template space.
The subworkflow relies on three parameters to be set:
- params.template: the template to use (e.g., ‘MNI152NLin2009cAsym’)
- params.templateflow_home: the path to the templateflow home directory. will be used to store the templateflow templates or to fetch them if they were already downloaded.
- params.template_res: the resolution of the template (e.g., 1)
- params.template_cohort: the cohort of the template (e.g., 1)
An example of how to set the module’s ext.args can be find in the
test/nextflow.config file.
Keywords : template, TemplateFlow, registration
Inputs
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| ch_anat | file | Channel containing the anatomical image to use to compute the registration into template space. Structure: [ val(meta), path(anat) ] | true | *.{nii,nii.gz} |
| ch_nifti_files | file | Channel containing the NIfTI files to register into the template space. Structure: [ val(meta), [path(nifti1), path(nifti2), path(nifti3), …] ] | false | *.{nii,nii.gz} |
| ch_mask_files | file | Channel containing binary mask files to transform in the template space. Structure: [ val(meta), [path(mask1), path(mask2), path(mask3), …] ] | false | *.{nii,nii.gz} |
| ch_labels_files | file | Channel containing label files to transform in the template space. Structure: [ val(meta), [path(label1), path(label2), path(label3), …] ] | false | *.{nii,nii.gz} |
| ch_trk_files | file | Channel containing the TRK files to register into the template space. Structure: [ val(meta), [path(trk1), path(trk2), path(trk3), …] ] | false | *.trk |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| ch_t1w_tpl | file | Channel containing the T1w template. Structure: [ path(t1w) ] | *.{nii,nii.gz} |
| ch_t2w_tpl | file | Channel containing the T2w template. Structure: [ path(t2w) ] | *.{nii,nii.gz} |
| ch_registered_anat | file | Channel containing the registered anatomical image into the template space. Structure: [ val(meta), path(anat) ] | *.{nii,nii.gz} |
| ch_registered_nifti_files | file | Channel containing the registered NIfTI files into the template space. Structure: [ val(meta), [path(nifti1), path(nifti2), path(nifti3), …] ] | *.{nii,nii.gz} |
| ch_registered_trk_files | file | Channel containing the registered TRK files into the template space. Structure: [ val(meta), [path(trk1), path(trk2), path(trk3), …] ] | *.trk |
| versions | file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
Components
- registration/ants
- registration/antsapplytransforms
- registration/tractogram
- image/applymask
- betcrop/fslbetcrop
- utils/templateflow
Authors
@gagnonanthony
Maintainers
@gagnonanthony
Last updated : 2025-07-15