Hoffman2:Modules
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
- SSH into Hoffman2
- Use your favorite text editor (e.g. vim) to edit the file
~/.bash_profile
$ vim ~/.bash_profile
- 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
- Type
- Save the file by typing
ESC + ":wq" + ENTER
- 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.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load afni
- To run AFNI, enter:
afni
ANTs
ANTs (Advanced Normalization Tools) computes high-dimensional mappings to capture the statistics of brain structure and function.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load ants
- Please see the ANTs website for usage examples.
Caret
Caret is a free, open-source, software package for structuraland functional analyses of the cerebral and cerebellar cortex.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load caret
- To run Caret, enter:
caret5
FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data..
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load fsl
- 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
ITKGray
ITKGray is a segmentation tool adapted and developed from ITKSnap by Bob Dougherty. ITKGray is a branch of the ITKSnap project. Bob added functionality from MrGray-Retired, including topology checking/fixing and a new flood-fill paintbrush that is similar to the MrGray-Retired auto-segmentation methods, but is run on small sections of an image rather than the entire image at once.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load itkgray
- To run ITKGray, enter:
itkgray
CCN supports several versions of ITKGray on Hoffman2. To see the list of available ITKGray versions, enter:
module av itkgray
To load a non-default version of ITKGray, enter (for example):
module load itkgray/080128
ITK-SNAP
ITK-SNAP ITK-SNAP is a software application used to segment structures in 3D medical images.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load itksnap
- To run ITK-SNAP, enter:
itksnap
CCN supports several versions of ITK-SNAP on Hoffman2. To see the list of available ITK-SNAP versions, enter:
module av itksnap
To load a non-default version of ITK-SNAP, enter (for example):
module load itksnap/3.4.0.QT4
FreeSurfer
FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.
- SSH into Hoffman2
- Start an interactive session on a compute node with qrsh. Then at the compute node shell prompt, enter:
module load freesurfer
- 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