tractogram_math

This module performs mathematical operations on tractograms. It can be used to concatenate multiple tractograms into a single file, compute the union of multiple tractograms, or perform other operations.
The available operations are:
- Concatenate: Combine multiple tractograms into a single file.
- Union: Compute the union of multiple tractograms.
- Intersection: Compute the intersection of multiple tractograms.
- Difference: Compute the difference between two tractograms.
- Lazy Concatenate: Concatenate multiple tractograms without loading them into memory.

Keywords : tractogram, math, concatenate

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Inputs

Input 1

Format : tuple val(meta), path(trks), path(reference)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
trks	file	List of tractograms to perform the operation on. e.g. [ path(trk1), path(trk2), path(trk3), ...]	True	*.trk
reference	file	Reference tractogram to use for the operation. e.g. [ path(reference) ]	False	*.{nii,nii.gz}

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Outputs

trk

Format : tuple val(meta), path(*.trk)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*.trk	file	Resulting tractogram after the operation. e.g. [ path(trk) ]	True	*.trk

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
operation	string	The mathematical operation to perform on the tractograms. e.g. concatenate, union, intersection, difference, lazy_concatenate	“	- concatenate - union - intersection - difference - lazy_concatenate
suffix	string	Suffix to add to the output tractogram file name.	“
precision	number	Precision used to compare streamlines.	4
robust	boolean	Use version robust to small rotations/translations.	False
no_metadata	boolean	Strip the streamline metadata from the output.	False
fake_metadata	boolean	Skip the metadata verification, create fake metadata if missing, can lead to unexpected behavior.	False
save_indices	string	Save the streamline indices to the supplied json file. The string in this argument will be used as the prefix of the output .json file.	“
save_empty	boolean	If set, we will save all results, even if tractogram if empty.	False
no_bbox_check	boolean	Activate to ignore validity of the bounding box during loading / saving of tractograms (ignores the presence of invalid streamlines).	False

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @gagnonanthony

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Last updated : 2026-02-12