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) for the bundle masks. Therefore, in this subworkflow, we apply a lower threshold to the TDI images to create binary bundle masks. The threshold values are based on recommendations from the IIT authors. 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

Outputs

	Type	Description	Mandatory	Pattern
bundle_masks	file	List of IIT binary bundle masks. Structure: `[ path(img), path(img), ... ]`	True	`*.nii.gz`
b0	file	Mean B0 map of the IIT Human Brain Atlas. Structure: `[ path(img) ]`	True	`*_b0.nii.gz`
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