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nf-neuro

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 maps/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, utils_options

Inputs

Section titled “Inputs”
TypeDescriptionMandatoryPattern
ch_subject_referencefileReference image from each subject on which the atlas’ reference image will be registered. This image is in the subject’s DWI space.

Structure : tuple val(meta), path(b0)
  • meta [map] Metadata map.
  • b0 [file] B0 image for a subject in the subject’s DWI space.
True*.nii.gz
ch_metricsfileList of metric maps for each subject in the subject’s DWI space.

Structure : tuple val(meta), path(metrics)
  • meta [map] Metadata map.
  • metrics [file] List of metric maps for a subject in the subject’s DWI space.
True*.nii.gz
optionsmapMap of options for the subworkflow.
  • use_atlas_iit (boolean) [Default: False]
    If ‘true’, the IIT Human Brain Atlas will be used for ROI metrics extraction.
  • atlas_iit_b0 (string) [Default: None]
    Path to a Mean B0 map of the IIT Human Brain Atlas. This input will be used instead of downloading the Mean B0 map if use_atlas_iit is set to ‘true’.
  • atlas_iit_bundle_masks_dir (string) [Default: None]
    Path to a directory containing IIT bundle masks. This input will be used instead of downloading and processing the bundle masks if use_atlas_iit is set to ‘true’.
  • use_binary_masks (boolean) [Default: False]
    If ‘true’, the IIT bundle masks will be thresholded to create binary masks before extracting the metrics.
True

Outputs

Section titled “Outputs”
TypeDescriptionMandatoryPattern
jsonfileList of binary bundle masks.
Structure : tuple val(meta), path(img)
  • meta [map] Metadata map.
  • img [file] List of binary bundle masks in the subject’s DWI space.
True*.nii.gz
stats_tab_meanfileStructured 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 : tuple val(meta), path(tab_mean)
  • meta [map] Metadata map.
  • tab_mean [file] Mean statistics table file.
True*_desc-mean_*.\{csv,tsv\}
stats_tab_stdfileStructured 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 : tuple val(meta), path(tab_std)
  • meta [map] Metadata map.
  • tab_std [file] Standard deviation statistics table file.
True*_desc-std_*.\{csv,tsv\}
versionsfileFile containing software versions

Structure : tuple path(versions)
  • versions [file] Versions YAML file.
Trueversions.yml

Authors

Section titled “Authors”

Maintainers

Section titled “Maintainers”

Last updated : 2026-03-17