Linux

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:

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

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

Conda (Miniforge)#

Note

Due to recent changes in the Terms of Service for the default channel in Anaconda, which puts our users at risk of legal action, the instructions below are for installing miniforge. This is a fork of miniconda that uses the conda-forge channel by default instead. It also uses mamba as its installer, instead of the native conda installer; this can greatly speed up environment set-up. See this SCT issue for further details on why you should use miniforge instead of miniconda for your Python environment management needs.

To install conda (via miniforge) on your computer:

  1. Download the miniforge installation script for your Linux distribution; you can find their latest release here (if you don’t know which file to get, try the x86_64 release first).

  2. Open a new shell, and run the following command:

bash Miniforge3-*.sh
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