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


This section covers workflows to assist the Neuroimaging Community.

MASSIVE, hosts the following Neuroimaging data collections with interest to host more data sets that are valuable to the community. If you would like us to consider hosting a data collection please see Requesting a data collection.

Available data collections on M3


Date of download

Human Connectome Project Dataset (HCP): HCP-1200 link


Lifespan Human Connectome Project Development (HCP-D) link


May 2021

Lifespan Human Connectome Project Aging link


May 2021

Baby Connectome Project link


Dec 2021

Human Connectome Project for Early Psychosis link


Aug 2021

Developing Human Connectome Project (dHCP) link


Aug 2021

Brain Genomics Superstruct Project link



Nathan Kline Institute Rockland Sample (NKI-RS): Neuroimaging Release link



Using SLURM to submit a simple FSL job#

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


  • 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…


Data and scripts#

  • 6 T1-weighted structural images

  • 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

Try to use

squeue -u (your_masssive_accName)

to check the job.


Output log files:

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


Output data:

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