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Setting up your linux environment

Owned by Maximilien CHAUMON
Last updated: Feb 14, 2022

Prerequisite

You must have an account on the network, and a linux home. See with your supervisor if it is not the case.

Goal of this tutorial

Setup your environment so that whenever you open a terminal, it looks decent and has a number of useful shortcuts enabled.

Step-by-step guide

  • Laurent HUGUEVILLE: to update 
  • L'utilisateur en question doit pouvoir accéder à /network/lustre/iss02/cenir/analyse/meeg/10_SCRIPTS/skel_meeg/setup_meeg.sh Laurent HUGUEVILLE

Open a terminal and type

$ /network/lustre/iss02/cenir/analyse/meeg/10_SCRIPTS/skel_meeg/setup_meeg.sh

Following this, close the terminal and open a new one. The command `manip YOUR_MANIP` will move you directly to your experiment"s folder:

Last login: Thu Jun  4 15:28:02 2020 from 10.255.255.18
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
user.name@icm-meg-le41 ~ $ 
user.name@icm-meg-le41 ~ $ manip SOLID_SOURCES
user.name@icm-meg-le41 /network/lustre/iss01/cenir/analyse/meeg/SOLID_SOURCES $