Attention

This documentation is under active development, meaning that it can change over time as we refine it. Please email help@massive.org.au if you require assistance, or have suggestions to improve this documentation.

Neuroimaging

This section covers workflows to assist the Neuroimaging Community.

Human Connectome Project Data Set

MASSIVE hosts a copy of the Human Conectome Project (HCP) Data, 900 and 1200 subject series. This data is restricted to M3 users that have their email registered with HCP (i.e. an account) AND have accepted the HCP terms and conditions associated with the datasets.

The data is located at:

/scratch/hcp
/scratch/hcp1200

The following outlines the process of getting access to this data:

Human Connectome Project Steps for Access

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

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 Diffusion)

MASSIVE Steps for Access

Request Access to HCPdata

If you have completed the Human Connectome Project steps above you can request access with this link: HCPData.

We will verify your MASSIVE email against the HCP site and grant access.

Accessing the Data

The data is available on M3 via /scratch/hcp and /scratch/hcp1200 You can also create a symbolic link to this in your home directory using

ln -s /scratch/hcp ~/hcp
ln -s /scratch/hcp1200 ~/hcp1200

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 SLURM to submit a simple FSL job

Example data at /home/chaos/kg98/chaos/SLURM/first/example

Background

  • FIRST is a simple tool in the FSL library to segment sub-cortical regions of a structural image.

  • It usually takes 20 minutes to process each image.

  • The typical output is a group of image masks of all sub-cortical regions, e.g., hippocampus, amygdala…

../_images/image2.png

Data and scripts

  • 6 T1-weighted structural images

    ../_images/image4.png
  • Three files in the script directory

    • Id.txt = base name list of these imaging files (check basename function for further help)

    • First_task.txt = file with the resource and environment detail of one fsl-first job NEED TO change the DIR for the correct path of input data

    • Submit_template= loop to submit all six jobs.

To run the job, simply do

$bash submit_template
../_images/image3.png

Try to use

squeue -u (your_masssive_accName)

to check the job.

../_images/image6.png

Output log files:

  • Log files should appear in the script folder, recording all the logs of fsl-first command

../_images/image5.png

Output data:

  • Output data should start to pop up in the data folder

../_images/image1.png