Skip to content

mrfil/pipeline-hpc

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

pipeline-hpc: Pipeline for processing DICOMs to resting-state functional connectivity and structural connectivity matrices and basic network-based statistics via BIDS App Singularity containers on Bright 9 HPCs. Pre-release beta version.

Requirements:

Singularity BIDS apps (HeuDiConv, MRIQC, fMRIPrep, xcpEngine, QSIprep)

Singularity image of Matlab R2019a (how to: https://github.com/mathworks-ref-arch/matlab-dockerfile)

Singularity image of Ubuntu with JQ installed Singularity image of Python3 (Based on Docker python/3.9.0)

Singularity image of Docker HTML to PDF (https://github.com/pinkeen/docker-html-to-pdf)

Brain Connectivity Toolbox for Matlab (https://sites.google.com/site/bctnet/Home/functions/BCT.zip?attredirects=0)

xcpEngine dsn files (https://github.com/PennBBL/xcpEngine/tree/master/designs)

Documentation

Visit our readthedocs site for more details https://pipeline-hpc.readthedocs.io/en/latest/About.html

HTML Report Tools

Python-based Quality Control report generator developed by Nishant Bhamidipati and Paul Camacho (https://github.com/mrfil/html-qc-reports):

git clone https://github.com/mrfil/html-qc-reports.git