Linux

Automatic Mount on Startup

For the following steps you need admin permissions.

1. Create data_processing & data_shared folders in /mnt, type:

sudo mkdir /mnt/data_processing
sudo mkdir /mnt/data_shared

2. Edit mount table, type : sudo nano /etc/fstab

3. For the following operating systems:

Ubuntu 14.04 LTS

Add the following lines at the bottom of the file:

#data_processing @SERVER
//IP_SERVER/data_processing        /mnt/data_processing    cifs    username=XXX,password=XXX    0       0

#data_shared @SERVER
//IP_SERVER/data_shared        /mnt/data_shared    cifs    username=XXX,password=XXX    0       0

Debian Wheezy 8

Add the following lines at the bottom of the file:

#data_processing @SERVER
//IP_SERVER/data_processing    /mnt/data_processing    cifs  nounix,sec=ntlmssp,user=XXX,password=XXX 0 0

#data_shared @SERVER
//IP_SERVER/data_shared    /mnt/data_shared    cifs  nounix,sec=ntlmssp,user=XXX,password=XXX 0 0

4. Remount drives and type: sudo mount -a

CentOS/Fedora/Red Hat

Ants & c3d

Binaries for debian work well, just make sure the paths are set in the bashrc as follow:

PATH=${PATH}:${SCT_DIR}/install/debian/ants

PATH=${PATH}:${SCT_DIR}/install/debian/c3d

FSL

Need libmng installed for fslview:

~ sudo yum install libmng libpng12

Then install FSL with the python script fslinstaller.py you’ll find there : http://goo.gl/Tfu1UW Make sure the installer set your bash configuration, following lines should be in your bashrc or bash_profile. If not, add it:

FSLDIR="/usr/local/fsl"
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

Miniconda

Run the miniconda installer shell script for linux you can get there http://conda.pydata.org/miniconda.html

~ bash Miniconda-*.sh

Then, in the SCT repo, type:

~ bash ./requirements/requirements.sh