Hoffman2:Modules

Back to all things Hoffman2

Environmental modules allow users to dynamically modify their shell environment (e.g., $PATH, $LD_LIBRARY_PATH, etc.) in order to support a number of applications installed on the Hoffman2 Cluster. CCN supports several modules on Hoffman2 including: AFNI, ANTs, Caret, FreeSurfer, FSL, ITKGray, ITK-SNAP, and MRIcron

Enabling the CCN Hoffman2 modules

1. SSH into Hoffman2
2. Use your favorite text editor (e.g. vim) to edit the file ~/.bash_profile

   • $ vim ~/.bash_profile

3. Insert these lines at the bottom of the file

   • Type G - (capital G) to go to the end of the file
   • Type A - (capital A) to go to the end of the line and enter insert mode
   • Type ENTER - to insert a newline
   • Type or paste in the lines below.

   • module use /u/project/CCN/apps/modulefiles
     umask 007

4. Save the file by typing

   • ESC + ":wq" + ENTER

5. Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

CCN Hoffman2 modules

AFNI

AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

1. SSH into Hoffman2
2. Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:

   module load afni

3. To run AFNI, enter:

   afni

ANTs

ANTs (Advanced Normalization Tools) computes high-dimensional mappings to capture the statistics of brain structure and function.

1. SSH into Hoffman2
2. Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:

   module load ants

3. Please see the ANTs homepage for usage examples.

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data..

1. SSH into Hoffman2
2. Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:

   module load fsl

3. To run FSL, enter:

   fsl

CCN supports several versions of FSL on Hoffman2. To see the list of available FSL versions, enter:

module av fsl

To load a non-default version of FSL, enter (for example):

module load fsl/4.1.9

FreeSurfer

FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.

1. SSH into Hoffman2
2. Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:

   module load freesurfer

3. To run (for example) freeview, enter:

   freeview

CCN supports several versions of FreeSurfer on Hoffman2. To see the list of available FreeSurfer versions, enter:

module av freesurfer

To load a non-default version of FreeSurfer, enter (for example):

module load freesurfer/4.4.0