atlas_iit

This subworkflow fetches and processes the IIT Human Brain Atlas including the mean B0 image and bundle masks. The authors of the IIT WM atlas only provide track density images (TDI) which can be used to create binary bundle masks by applying a threshold. Therefore, in this subworkflow, we offer the option to apply such a threshold (with the values recommended by the IIT authors) to create binary bundle masks, or to simply output the TDI bundle maps which can also be used as weighted representations of the bundles for downstream analyses (e.g. for extracting metrics weighted by the TDI values). For more information about the atlas and the recommended thresholds, please refer to this link

The user can also provide their own Mean B0 map and/or bundle masks directory, using the parameters params.atlas_iit.b0 and params.atlas_iit.bundle_masks_dir, respectively. If provided, the subworkflow will use these inputs instead of downloading and processing them, which is particularily useful for processing on HPC.

The Mean B0 maps as well as the bundle density maps used are in 182x218x182 matrix size. The Atlas is in the MNI152NLin6Asym template space (1mm resolution).

Keywords : atlas, iit, neuroimaging, bundles, template

Components : image/math, utils_options

Inputs

	Type	Description	Mandatory	Pattern
options	map	Map of options for the atlas_iit subworkflow. threshold_bundles (boolean) [Default: False] If enabled, this will threshold the TDI bundle maps with the recommended thresholds to create binary bundle masks. If disabled, the subworkflow will output the TDI bundle maps. smooth_sigma (float) [Default: 1.0] If `threshold_bundles` is enabled, this will apply a gaussian smoothing with the specified sigma to the TDI bundle maps before thresholding. This is based on the recommendation of the IIT atlas authors to apply some smoothing to the TDI maps before thresholding. atlas_iit_b0 (string) [Default: None] 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. atlas_iit_bundle_masks_dir (string) [Default: None] Path to a directory containing IIT bundle masks. If provided, these inputs will be used instead of downloading and processing the bundle masks.	False

Outputs

	Type	Description	Mandatory	Pattern
bundle_masks	file	List of IIT binary bundle masks. Structure : `tuple path(bundle_masks)` bundle_masks [file] List of IIT binary bundle mask files.	True	`*.nii.gz`
b0	file	Mean B0 map of the IIT Human Brain Atlas. Structure : `tuple path(b0)` b0 [file] Mean B0 image file.	True	`*_b0.nii.gz`
versions	file	File containing software versions Structure : `tuple path(versions)` versions [file] Versions YAML file.	True	`versions.yml`

Authors

@levje

Maintainers

@levje

Last updated : 2026-03-17