Data Processing and Hosting Resources
A state-of-art mini cluster platform provided to our users and collaborators for data processing and hosting.
The CSIC Core is equipped with a state-of-the art computing facility consisting of a 25 nodes linux mini cluster (including two backup nodes), disk RAIDs with 1 PiB total data storage capacity, a full rack capable of supporting up to 16U calculation nodes, and an automated 1 PiB back-up system. It consists of 3 head nodes/file servers, one of them is enhanced with dual NVIDIA A40 GPUs, 9 CPU intensive calculation nodes, 5 GPU enhanced nodes with NVIDIA P100 and A40 GPUs, 4 NVIDIA Quadro P1000 accelerated CPU nodes, 1 special purpose workstation, and 3 backup nodes. For data processing and analysis, Matlab, IDL, LCmodel, SPSS, SPM, fsl, AFNI, freesurfer, and multiple python and R based pipelines are installed and available on our cluster. VMware and Oracle VirtualBox are also available for special virtualization need. The computer cluster is also a dicom receiving server open to all collaborating PIs for data storage and analysis purpose.
The calculation nodes support 936 simultaneous CPU threads with 3-12GB per threads RAM. The GPU nodes are equipped with 3x P100 GPUs and 10x A40 GPUs.
The CSIC computer cluster is currently hosting MRI data collected from all CSIC MRI scanners, the MRI scanner operated by FERN, and PET/CT data from the CSIC PET/CT scanner. It also hosts data processing for our collaborating teams with not only data generated from the above listed facilities, but also data acquired by Emory National Primate Research Center, and imported data by collaborating projects from 10+ sites nationwide.
Data Processing and Hosting Services
CentOS 7.6 on node 1, and 23.
Rocky Linux 8.4 on node 2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,18,19,20,21,22,24,25, and 26.
Rocky Linux 9.1 on node 27 and 28.
Node9 is pending replacement.
GCC: Red Hat 4.9.2.6 (devtoolset-3); Red Hat 6.3.1-3 (devtoolset-6); Red Hat 7.3.1-5 (devtoolset-7); Red Hat 8.2.1-3 (devtoolset-8); Red Hat 8.3.1-4 (CentOS 8.1)
Python: 2.7 native for CentOS7 nodes; 3.6.3 optional for CentOS7 nodes with Spyder 4.1.1; 3.6.8 native for Rocky Linux nodes with Spyder 4.1.1.
R: 3.6.0 on CentOS7 nodes, 4.1.0 on Rocky Linux nodes.
4dfp: A functional neuroimaging data format and tool box.
AFNI: AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data.
ANTs: Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. ANTs development is led by Brian Avants and supported by other researchers and developers at PICSL and other institutions.
ctn: Central Test Node Dicom Tools
dcmtk: DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
freesurfer: An open source software suite for processing and analyzing (human) brain MRI images.
fsl: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).
lapack: Linear Algebra PACKage
lcmodel: (node7 only) Automatic quantification of in vivo proton MR spectra.
Mango: Multi-image Analysis GUI – is a viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.
mirtk: The MIRTK is a research-focused image processing toolkit, developed at the BioMedIA research group. It provides a collection of libraries and command-line tools to assist in processing and analyzing imaging data.
mricron: MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.
MRTrix: MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
NiftyFit: NiftyFit is an open-source software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI.
PANDA: PANDA (Pipeline for Analyzing braiN Diffusion imAges) is a matlab toolbox for pipeline processing of diffusion MRI images.
Slicer: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community.
SPM: Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in a free and open source software that is called SPM.
tarquin: TARQUIN is an analysis tool for automatically determining the quantities of molecules present in MR spectroscopy data.
workbench: Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.