Hoffman2:Modules

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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,FSL, FreeSurfer, ITKGray, ITK-SNAP, and MRIcron.

Enabling the CCN Hoffman2 modules

  1. SSH into Hoffman2
  2. Use gedit or your favorite text editor (e.g. nano or vim) to edit the file ~/.bashrc
    • $ gedit ~/.bashrc
  3. Insert these lines at the bottom of the file
    • module use /u/project/CCN/apps/modulefiles
      umask 007
  4. Important: remove or comment out these lines (if present):
    • # Remove or comment out this line!
      #source /u/project/FMRI/apps/etc/profile
    • # Remove or comment out this line!
      #umask 0022
  5. Save the file
  6. 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 website for usage examples.

Caret

Caret is a free, open-source, software package for structuraland functional analyses of the cerebral and cerebellar cortex.

  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 caret
  3. To run Caret, enter:
    caret5

DCMTK

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

  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 dcmtk
  3. To run (for example) dcmdump, enter:
    dcmdump [options] dcmfile(s)

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/5.0.7

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/5.1.0

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.

  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 itkgray
  3. 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 is a software application used to segment structures in 3D medical 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 itksnap
  3. 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

MRIcron

MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.

  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 mricron
  3. To run MRIcron, enter:
    mricron

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

module av mricron

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

module load mricron/20150622

CCN Scripts

Load the ccnscripts module to run CCN-supported scripts on Hoffman2: setup_subject, :setup_subject, fix_perms.sh, etc.

  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 ccnscripts