LQT Pipeline

Using the Lesion Quantification Toolkit (LQT) to quantify lesion disconnection.

Last updated: 2025-08-02, WYJ

__init__

LQT Pipeline for lesion disconnection analysis.

Parameters:

Name	Type	Description	Default
subject	BIDSSubject	A BIDS subject object.	required
session	BIDSSession	A BIDS session object.	required
output_path	str	Directory to save outputs.	required
seed_mask	str	Name of the seed mask folder in 'derivatives'. For example, if the ROI mask path is 'derivatives/lesion_mask/sub-XXX/ses-XXX/*infarction.nii.gz', then seed_mask='lesion_mask'.	'lesion_mask'
use_which_mask	str	Keyword to select the desired lesion mask. Default is 'infarction'. For example, if the lesion mask is 'derivatives/lesion_mask/sub-XXX/ses-XXX/*infarction.nii.gz', then use_which_mask='infarction'.	'infarction'
extract_from	str	If extracting results, please provide it.	None

check_data_requirements

Will always return True, as the LQT pipeline will check the seed mask in MNI space during creation of the workflow.

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A more detailed description:

Source: LQT

Note

LQT is implemented in R, so you need to have R installed on your system. Using R in WSL seems to have some instability, try changing the cores=4 parameter in 'cvdproc/pipelines/r/lqt_single_subject.R'.

I recommend using the RStudio IDE (because we use rstudioapi in the script) and open 'cvdproc/pipelines/r/lqt_initialize.r' to initialize the LQT package: As the package is no longer being actively maintained, we included the package in 'cvdproc/pipelines/external/LQT' and we can install it from there. Then we need to copy some extension data to the package directory (data is in 'cvdproc/data/lqt/extdata'), which is done in the script. Doing this by following instructions in the LQT README seems incorrect as it will download a MacOS version of DSI Studio, which is not compatible with WSL Linux.