atlas_roimetrics

This subworkflow will compute the mean and standard deviation of each provided metric map for each bundle mask of the configured atlas. The subworkflow takes as input the reference image from each subject (e.g. the B0). The atlas template reference image is registered to the subject’s DWI space. The transformation is then applied on the bundle masks for each subject, allowing us to have the bundle masks in the same space as the input metric images (i.e. in the subject’s DWI space).

Keywords : atlas, bundles, neuroimaging, template, iit, roi, metrics, stats

Components : atlas_iit, registration/ants, stats/metricsinroi, registration/antsapplytransforms

Inputs

	Type	Description	Mandatory	Pattern
ch_subject_reference	file	Reference image from each subject on which the atlas’ reference image will be registered. This image is in the subject’s DWI space. Structure: `[ val(meta), path(b0) ]`	True	`*.nii.gz`
ch_metrics	file	List of metric maps for each subject in the subject’s DWI space. Structure: `[ val(meta),` [ path(metric1), path(metric2), … ] `]`	True	`*.nii.gz`
options	map	Map of options for the subworkflow. - use_atlas_iit (bool): If ‘true’, the IIT Human Brain Atlas will be used for ROI metrics extraction.	True

Outputs

	Type	Description	Mandatory	Pattern
json	file	List of binary bundle masks. Structure: `[ path(img), path(img), ... ]`	True	`*.nii.gz`
stats_tab_mean	file	Structured tabular (TSV or CSV) file holding MEAN metrics values for each bundle mask. The tabular file has the following column structure: (sample, roi, metric1, metric2, …, metricN). Structure: `[ val(meta), path(tab_mean) ]`	True	`_desc-mean_.{csv,tsv}`
stats_tab_std	file	Structured tabular (TSV or CSV) file holding STANDARD DEVIATION metrics values for each bundle mask. The tabular file has the following column structure: (sample, roi, metric1, metric2, …, metricN). Structure: `[ val(meta), path(tab_std) ]`	True	`_desc-std_.{csv,tsv}`
versions	file	File containing software versions Structure: `[ path(versions.yml) ]`	True	`versions.yml`

Parameters (see configuration)

	Type	Description	Default	Choices
atlas_iit_b0	string	Path to a Mean B0 map of the IIT Human Brain Atlas. If provided, this input will be used instead of downloading the Mean B0 map. Structure: path(img)	None
atlas_iit_bundle_masks_dir	string	Path to a directory containing IIT bundle masks. If provided, these inputs will be used instead of downloading and processing the bundle masks.	None

Authors

@levje

Maintainers

@levje

Last updated : 2025-12-22