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)

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

Table of contents

• Installation
  • Dependancies
  • Install skullTo3d package
  • Testing the install
• Container install
  • Dockerfile
  • Docker image
  • Note on Singularity
• Launching a processing
  • Commands
  • Expected input data
  • Command line parameters
• Parameters
  • Adding -params
  • Advanced parameters settings
• Individual Parameters
  • Adding -indiv
  • Advanced parameters settings