7T-pipeline-hpc: Pipeline for processing 7T brain MRI DICOMs to resting-state functional connectivity and structural connectivity matrices, basic network-based statistics, hippocampal subfield segmentation via BIDS App Singularity containers on HPCs.

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 and JO 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)

ASHS (https://sites.google.com/site/hipposubfields/)

LAYNII (https://github.com/layerfMRI/LAYNII)

bidsphysio (https://github.com/cbinyu/bidsphysio)

Documentation

Visit our readthedocs site for more details https://7t-mri-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