Tool to simplify the automation of freesurfer using docker on a server

Introduction

Installation

git clone https://github.com/edo98811/fs-docker.git
cd fs-docker-manager
pip install (-e) .

e for developement installation

Preparation

The folder where this is run needs to hafve a regular structure, acquisition folder and files inside. the files canbe nifti or dicom, name of the acquisition folder is the one used in the table

Commands

• fs_docker init_config Requires one argument, path to the new config file that needs to be created, it needs to be a .json file Arguments: string, path to config file, including the name of the file, the name needs to be ajson file. example: "/mnt/S/edoardoStorage/config.json"

• fs_docker tool table To run first you need to run create table, it can be either done starting from nifti or from dicom, default is starting from dicom, when you want to start from nifti you need to use -start_type nifti. This creates a table that contains all the info on the subjects ordered in these columns: ID, mris, paths. Then according to the substrings given classifies the scans in categories-

• fs_docker tool fstables create the tables using the freesurfer command to get a summmary of all the processed images

• fs_docker tool register Register the t2 to the t1 to run the samseg

• fs_docker tool preparenifti move the nifti files to another folder if the nifti folder is different from rawdata folder in settings, otherwise converts the dicom folder to nifti if needed

• fs_docker tool convertdicom convert the dicom files to nifti

• fs_docker tool samseg run samseg, to be run after performing the registration

Workflow example:

install package

fs_docker init_config

set in settings the parameters and the substrings to to check for matching

fs_docker tool table 
fs_docker tool convertdicom

or

fs_docker tool table --start_type nifti

Then

fs_docker tool reconall 

or

fs_docker tool registration 
fs_docker tool samseg

Configuration File Description

This file is used for set up the program for the current dataset

Paths

• nifti: The path to the directory containing NIfTI files.
• rawdata: The path to the directory containing rawdata files, can also be the same as nifti.
• base_path: The base directory path for various tools and outputs.
• dicom: The path to the directory containing DICOM files.
• reconall: The path to the directory for recon-all results.
• samseg: The path to the directory for SAMSEG results.
• license_path: The path to the license file.
• table_path: The path to the directory for table results.
• table_name: The name of the table file.

File Identifiers

• file_identifiers: A dictionary containing identifiers for different types of MRI files.
  • T1: Identifiers for T1 MRI files.
  • T2: Identifiers for T2 MRI files.
  • FLAIR: Identifiers for FLAIR MRI files.
  • T1_no: Identifiers for files that are not T1 MRI (selection by exclusion).
  • T2_no: Identifiers for files that are not T2 MRI.
  • FLAIR_no: Identifiers for files that are not FLAIR MRI.