SkullTo3D

skullTo3d is an upper layer of Macapype project, adding to MRI anatomocal brain segmentation skull segmentation, either originating from CT scan , MRI petra or T1w sequence, as well as angio images segmentation

Installation

See Quick Installation for installation on your local system if you have adequate softwares (i.e. FSL, AFNI, Ants, SPM) running on your machine/clusters

See Container installation for fully compliant installation (no MRI softwares, or Windows / MacOS operating system)

Once installed, see Quick test for testing if your installation is working properly

Command line parameters

SkullTo3D is fairly flexible, but requires to specify multiples parameters in command line

See Commands for a description on the avalaible command parameters

If -deriv` is provided, see Derivatives for a descrition of the outputs

Table of contents

• Installation
  • Dependancies
  • Install skullTo3d package
  • Testing the install
• Container install
  • Dockerfile
  • Docker image
  • Note on Singularity
• Quick test
  • Download datasets
  • Testing depending on the installation
  • Testing the macaque datasets with CT and petra
• Launching a processing
  • Commands
  • Expected input data
  • Command line parameters
• Derivatives
  • Introduction
  • Data Preparation (Padded files)
  • Petra Skull extraction
  • T1w Skull extraction
  • CT Skull extraction
• Parameters
  • Adding -params
  • Advanced parameters settings
• Individual Parameters
  • Adding -indiv
  • Advanced parameters settings