National Biomedical Imaging Archive (NBIA) Data Retriever
Overview
NBIA Data Retriever is a tool to download radiology images from The Cancer Imaging Archive (TCIA).
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | nbia-data-retriever/4.4.3-1 |
| BGSC | Not available |
Note: You can simply use module load nbia-data-retriever to activate the most recently installed version of this software.
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load gtdbtk # Load NBIA Data Retriever
nbia-data-retriever --cli <manifest directory path>/<manifest file name>.tcia -d <parent location>/<download directory> -l <location>/<credential file> -v –f
Real Example
Has your research group used NBIA Data Retriever in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
If you don't use any specific dataset but only TCIA in general please use the following citation.
Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/10.1007/s10278-013-9622-7
Other datasets within TCIA may have specific citation restrictions, find more information here.