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.

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 requestdata.

Available data collections on M3

Version

Date of download

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

2017-03-01

Brain Genomics Superstruct Project link

10.5

2020-09-10

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

RawDataBidsLatest

2020-08-19

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