JLF

The JLF pipeline produces a high-resolution anatomical segmentation using the ANTs Joint Label Fusion algorithm. A T1-weighted image is the only input needed.

Usage

The pipeline contains three stages: 1) Registration: registers atlas into participants' T1-weighted space, 2) antsjointfusion: segments T1 images using multi-atlas segmentation with joint label fusion, 3) Extraction: extracts ROI and lesion volumes.

This pipeline can be run with or without a container. For containerized usage, Singularity can be used on a cluster or Docker locally. This pipeline can be run in individual or batch mode, meaning you can specify a certain subject and session or run the pipeline for all subjects in the folder, respectively.

These examples will run the pipeline in batch mode on the cluster. To run individually or locally/with a container, set --mode individual, or -c local/-c singularity/-c docker, respectively. Only Steps 1 and 2 have the option of individual or batch; Step 3 will always run in batch mode.

Step 1. Registration

This step registers the selected atlas to the subjects' native T1 space.

Required flags:

-m or --mainpath: path to parent data folder
-t or --t1: T1 sequence name
-s or --step: step of pipeline - registration, antsjointfusion, extraction. Default is antsjointfusion. This step is registration
--toolpath: path to pipeline folder

Other flags:

-p or --participant: participant ID (only needed for individual mode)
--ses: session ID (only needed for individual mode)
-n or --num: number of templates. Default is 9
--type: type of templates - WMGM, thal. Default is WMGM
--lesion: extract lesion volumes. Default is TRUE
--mode: run pipeline individually or batch. Default is batch
-c or --container: which container to use: singularity, docker, local, cluster. Default is cluster
--sinpath: path to singularity image (only needed if using singularity container - don't need to specify if using takim cluster)
--dockerpath: path to docker image (only needed if using docker container)
-h or --help: show help message

bash /path/to/PennSIVE_neuro_pip/pipelines/JLF/code/bash/JLF.sh -m /path/to/project --t1 "*T1w*.nii.gz" --step registration --toolpath /path/to/PennSIVE_neuro_pip

Step 2. antsJointFusion

This step runs the antsJointFusion function from ANTs.

Required flags:

-m or --mainpath: path to parent data folder
-t or --t1: T1 sequence name
--toolpath: path to pipeline folder

Other flags:

-p or --participant: participant ID (only needed for individual mode)
--ses: session ID (only needed for individual mode)
-n or --num: number of templates. Default is 9
--type: type of templates - WMGM, thal. Default is WMGM
-s or --step: step of pipeline - registration, antsjointfusion, extraction. Default is antsjointfusion
--mode: run pipeline individually or batch. Default is batch
-c or --container: which container to use: singularity, docker, local, cluster. Default is cluster
--sinpath: path to singularity image (only needed if using singularity container - don't need to specify if using takim cluster)
--dockerpath: path to docker image (only needed if using docker container)
-h or --help: show help message

bash /path/to/PennSIVE_neuro_pip/pipelines/JLF/code/bash/JLF.sh -m /path/to/project --t1 "*T1w*.nii.gz" --toolpath /path/to/PennSIVE_neuro_pip

Step 3. Extraction

This step extracts ROI and lesion volumes for all participants and sessions.

Required flags:

-m or --mainpath: path to parent data folder
-s or --step: step of pipeline - registration, antsjointfusion, extraction. Default is antsjointfusion. This step is extraction
--toolpath: path to pipeline folder

Other flags:

-p or --participant: participant ID (only needed for individual mode)
--ses: session ID (only needed for individual mode)
--type: type of templates - WMGM, thal. Default is WMGM
--lesion: extract lesion volumes. Default is TRUE
--mode: run pipeline individually or batch. Default is batch
-c or --container: which container to use: singularity, docker, local, cluster. Default is cluster
--sinpath: path to singularity image (only needed if using singularity container - don't need to specify if using takim cluster)
--dockerpath: path to docker image (only needed if using docker container)
-h or --help: show help message

bash /path/to/PennSIVE_neuro_pip/pipelines/JLF/code/bash/JLF.sh -m /path/to/project --step extraction --toolpath /path/to/PennSIVE_neuro_pip