Multimodal lesion mapping in focal epilepsy with zbrains --------------------------------------------

zbrains is developed by MICA-Lab, affiliated with McGill University, the Montreal Neurological Institute and Hospital "the Neuro," and the McConnell Brain Imaging Center (BIC).

This open access processing and analysis tool aims identify patient-specific anomalies in brain morphology and microstructure, using features with previously demonstrated potential to accurately localize epileptogenic lesions. zbrains uses a set of known software dependencies developed by other groups and aggregated in a published pipeline micapipe.

Tutorial

You must be inside the zbrains repository to run the following commands.

cd /path/to/zbrains/repository

ZBRAINS=$(dirname "$(realpath "$0")")
source "${ZBRAINS}/functions/init.sh"

zbrains requires input and output directories:

• pth_dataset points to the BIDS-format dataset path where micapipe, hippunfold, and zbrains directories will be stored
• micapipe_dir contains the output of micapipe previously run on the BIDS dataset (also BIDS-format)
• hippunfold_dir contains the output of hippunfold previously run on the BIDS dataset (also BIDS-format)
• zbrains_dir points to the directory that will hold z-brains outputs

# path for dataset in BIDS structure
pth_dataset="/path/to/BIDS_dataset"

micapipe_dir="name_of_micapipe_folder"
hippunfold_dir="name_of_hippunfold_folder"
zbrains_dir="name_of_z-brains_folder"

Preparing control data

A .csv file with ID and session for healthy controls are required

# csv file with ID and session for control participants to be processed
demo_controls='/path/to/control/participants.csv'

To process features for healthy controls as a batch, run the following. Note that column names of the healthy controls .csv file must be specified under --column_map.

./zbrains_batch --run proc \
   --demo "${demo_controls}" \
   --dataset "${pth_dataset}" \
   --zbrains ${zbrains_dir} \
   --micapipe ${micapipe_dir} \
   --hippunfold ${hippunfold_dir} \
   --column_map participant_id=ID session_id=SES \
   --verbose 2 \
   --scheduler_options "-n 20" #specify threads here

Processing and analyzing patient features

# specify the list of subject IDs along with corresponding session
subject_ids=(sub-PX001 sub-PX002)
session_ids=(ses-01 ses-01)

# csv file with ID and session for control participants for comparison
demo_controls='/path/to/control/participants.csv'

    ./zbrains --run analysis \
              --sub "${sid}" \
              --ses "${ses}" \
              --dataset ${pth_dataset} \
              --zbrains ${zbrains_dir} \
              --demo_ref ${demo_controls} \
              --dataset_ref ${pth_dataset} \
              --zbrains_ref ${zbrains_dir} \
              --column_map participant_id=ID session_id=SES \
              --verbose 2