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.templateflow_res: the resolution of the template (e.g., 1)
params.templateflow_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. Additional configuration for local templates are also available in the test/local.config file.

To select the registration technique used to register the input files, use the following parameters :

params.run_easyreg : Use Easyreg any-to-any registration model
params.run_synthmorph : Use Synthmorph ML registration model

Refer to the registration subworkflow and the modules it uses for configuration options.

Keywords : template, TemplateFlow, registration

Components : registration/antsapplytransforms, registration/tractogram, image/applymask, betcrop/fslbetcrop, utils/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`
ch_freesurfer_license	file	ONLY USED WITH SYNTHMORPH REGISTRATION. The input channel containing the Freesurfer license file. Structure: `[ val(meta), path(license) ]`	False	`*.txt`

Outputs

	Type	Description	Mandatory	Pattern
ch_t1w_tpl	file	Channel containing the T1w template. Structure: `[ path(t1w) ]`	True	`*.{nii,nii.gz}`
ch_t2w_tpl	file	Channel containing the T2w template. Structure: `[ path(t2w) ]`	True	`*.{nii,nii.gz}`
ch_registered_anat	file	Channel containing the anatomical image registered into the template space. Structure: `[ val(meta), path(anat) ]`	True	`*.{nii,nii.gz}`
ch_registered_nifti_files	file	Channel containing the NIfTI files registered into the template space. Structure: `[ val(meta),` [path(nifti1), path(nifti2), path(nifti3), …] `]`	False	`*.{nii,nii.gz}`
ch_registered_mask_files	file	Channel containing the mask files registered into the template space. Structure: `[ val(meta),` [path(mask1), path(mask2), path(mask3), …] `]`	False	`*.{nii,nii.gz}`
ch_registered_labels_files	file	Channel containing the label files registered into the template space. Structure: `[ val(meta),` [path(label1), path(label2), path(label3), …] `]`	False	`*.{nii,nii.gz}`
ch_registered_trk_files	file	Channel containing the TRK files registered into the template space. Structure: `[ val(meta),` [path(trk1), path(trk2), path(trk3), …] `]`	False	`*.trk`
mqc	file	Channel containing the MultiQC report of the registration. Structure: `[ path(mqc) ]`	False	`mqc.`
versions	file	File containing software versions Structure: `[ path(versions.yml) ]`	True	`versions.yml`

Parameters (see configuration)

	Type	Description	Default
template	string	Name of the template to use (see https://templateflow.org).
templateflow_home	string	Path to the templateflow local home directory where files are located and/or downloaded.
templateflow_res	int	Template resolution to use or download.
templateflow_cohort	string	Name/type of the cohort to use.
run_easyreg	boolean	Use Easyreg any-to-any registration model.	False
run_synthmorph	boolean	Use Synthmorph ML registration model.	False

Authors

Maintainers

@gagnonanthony

Last updated : 2025-12-22