lin4neuro-xenial

Building script of Lin4Neuro based on Ubuntu-mini 16.04 (xenial)

This repository includes scripts to make Lin4Neuro from Ubuntu-mini.iso. It also includes installer-scripts for several neuroimaging software.

How to make Lin4Neuro with your own

Install Ubuntu-mini.iso

You can get iso of ubuntu 16.04 from http://archive.ubuntu.com/ubuntu/dists/xenial/main/installer-amd64/current/images/netboot/mini.iso

Install with this iso and select no packages during installation.

reboot the system and login.

Install the latest kernel for the version

linux-image-generic-hwe-16.04-edge is the latest kernel for xenial. Install this with the followings;

sudo apt update
sudo apt -y full-upgrade
sudo apt -y install linux-image-generic-hwe-16.04-edge

Install git and clone this repository

After installation, install git, make ~/git directory, and clone this repository under ~/git. (You can save this repository wherever you like.)

cd
LANG=C #if your LANG is other than English
sudo apt install git
mkdir git
cd git
git clone https://github.com/kytk/lin4neuro-xenial.git

Install the Lin4Neuro-base

First, run build-l4n-xenial-1.sh.

cd lin4neuro-xenial
./build-l4n-xenial-1.sh

The script will bring a prompt as following;

    Which language do you want to build? (English/Japanese)
    1) English
    2) Japanese
    3) quit
    #?

Choose 1 or 2 depending on your language.

Then XFCE4.12 is installed. Upon installation, the system automatically reboots.

Installation of Neuroimaging software packages

Then, run build-l4n-xenial-2.sh.

cd ~/git/lin4neuro-xenial
./build-l4n-xenial-2.sh

This will install several neuroimaging software packages listed below.

Version number is as of 9 Apr 2018.

3D Slicer 4.8.1
Aliza 1.38.2.6
C3D 1.0.0
DSI Studio compiled on 17 Mar 2018
ITK-SNAP 3.6.0
Mango 4.0.1
MRIcroGL 14-July-2017
MRIcron 12-Oct-2016
ROBEX v12
Virtual MRI

Check the software packages are installed correctly.

After installation of the software above, close and re-open the terminai. Then, run build-l4n-xenial-3.sh.

cd ~/git/lin4neuro-xenial
./build-l4n-xenial-3.sh

This script simply tries to run software listed above. If it is not installed correctly, you will see error messages in the terminal. Check it and correct.

Prepare for remastering

If everything is set, run build-l4n-xenial-4.sh.

./build-l4n-xenial-4.sh

This will install customized Remastersys. Since remastersys stops developing, we customized the remastersys so it works for our need.

Configuration of remastersys is found in /etc/remastersys.conf

Modify the setting as you wish.

Remastering

Now you are ready to remaster the system. Run l4n_remastering.sh

./l4n_remastering.sh

This will make an iso imagefile in /home/remastersys/remastersys.

You can share the iso with others.

Installer for other neuroimaging software packages

I also prepared the installer for popular software packages.

AFNI
ANTs
CONN 17f standalone
FreeSurfer
FSL
MRtrix3
SPM12 standalone

these installer can be found in lin4neuro-xenial/installer.