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Neuroimaging

This section covers workflows to assist the Neuroimaging Community.

Human Connectome Project Data Set

MASSIVE is hosting a copy of the Human Conectome Project (HCP) Data. This data is restricted to MASSIVE users that have their email registered with HPC (i.e. an account) AND have accepted the HCP terms and conditions associated with the datasets. The following outlines the process of getting access to this data:

Human Connectome Project Steps for Access

  1. Create an Account
    1. Follow the "Get Data" link to: http://www.humanconnectome.org/data/
    2. Select "Log in to ConnectomeDB"
    3. Select "Register"
    4. Create an account and make sure that your email address matches the email associated with you MASSIVE account
    5. You will recieve an email to validate your account
  2. Accept Terms and Conditions
    1. Login to https://db.humanconnectome.org/
    2. Accept terms and conditions using the "Data Use Terms Required" button on all 3 datasets (WU-Minn, WU-Minn HCP Lifespan Pilot and MGH HCP Adult Diffiusion) 

MASSIVE Steps for Access

  1. Request Access to HCPdata
    1. If you have done the Human Connectome Project steps above you can request access with this link: HCPData
    2. We will verify your MASSIVE email against the HCP site and grant access
  2. Accessing the Data
    1. The data is available on M2 via /gpfs/M2Scratch/hcp
    2. You can also create a symbolic link to this in your home directory using ln -s /gpfs/M2Scratch/hcp ~/hcp

Note: The Connectome Workbench is available via the MASSIVE Desktop. Any updates to this or other software requirements can be directed to help@massive.org.au

Using and Customising SPM and Toolboxes

SPM is a MATLAB toolbox for Statistical Parametric Mapping of spatially extended statistical processes for functional imaging data. General instructions on using MATLAB and toolboxes is covered here.

SPM has additional complications in that 1) it itself contains toolboxes 2) it is patched regularly (rather than having version releases). On MASSIVE we use the following process for managing SPM.

  • SPM is a module, which is installed outside of the MATLAB installation
  • A module is created for each installed SPM version and update e.g. spm8/r4290
  • The SPM install includes any subtoolboxes that users have requested (e.g. vbm8)
  • As updates to SPM are requested, the entire previous install is copied (i.e. including subtoolboxes) and the updates are applied.
  • Each install is given its own unique module
  • The latest version will therefore have the most complete set of toolboxes
  • Users should therefore take care that they are selecting the correct version for their needs. As described in the MATLAB section users can also create a custom SPM by copying the entire toolbox install into their project directory and setting the paths accordingly. MASSIVE help can provide assistance is setting this up.

Neuro Modules

To assist neuroimaging researchers in getting started with MASSIVE we are providing preconfigured modules that give a starting point for completing tasks on MASSIVE. The modules available can be found with the command "module avail neuro". Over time more modules and information about using these modules will be included in the user guide. As a starting point a first module (neuro/spm8) simply configures SPM in a standard configuration. To see what the modules do, use the "module show" command.

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