Welcome to LOBI inhouse resources documentation!

Materials contained here should help you with using our computer resources, most notably Calcus computational server.

Calcus:

• Calcus: the basics
  • SSH (connecting remotely)
  • Drives
• The command line: bash & SSH
  • Bash (the command line interface)
  • Getting Bash
  • SSH
• Transferring data
  • SCP
  • Rsync
  • Samba
• Tmux
  • Introduction
  • The very basics
  • Usage
  • References
• Software
  • List
  • Freesurfer
  • mrtrix
  • ANTs
  • Python
• Singularity
  • The basics
  • Use case: BIDS Apps
  • Use case: Neurodocker
  • References
• Matlab
  • How to use
  • Multivariate and Repeated Measures for Neuroimaging (MRM)
  • Matlab & GNU Parallel
  • Things to keep in mind
• Nipype
  • Installation and configuration
  • Use case: smoothing fmriprep derivatives with spm
  • References
• Tips & Tricks
  • Htop
  • SSH
  • Bash keyboard shortcuts
• Admin actions
  • Adding users
  • MOTD
• Contributing to the Docs

MRI primer:

• MRI primer
  • PACS
  • OsiriX and Horos
  • XNAT
• Access MRI data
  • Log into XNAT
  • Find your project
  • Download your data
• Work with MRI data
  • Convert to NIfTI
  • Convert to BIDS

Other resources:

• QNAP Network Attached Storage