qmri-neuropipe

Remove carriage returns (\r) from the file.

It has four different pipelines (anatomical, diffusion, relax, segmentation).

Currently the starting point is nifti files organized according to BIDS.

Required software (basic installation)

• CMake
• Anaconda
• FSL
• AFNI
• HD-BET

To install and activate qmri conda-environment:

git clone https://github.com/Developing-Brain-Imaging-Lab/qmri-neuropipe.git qmri-neuropipe --recurse-submodules
cd qmri-neuropipe
conda env create -f environment.yml
conda activate qmri

Python Packages Used

• ANTS
• ANTSPyNET
• MRtrix3
• DIPY
• DMIPY
• DMRI-AMICO
• TractSeg

Basic use cases

DTI

./qmri-neuropipe.py --load_json testing/dti-proc-config.json --subject 10021 --session 01

NODDI

CSD

Connectomes

TODOs

• help pages for each specific pipeline
• starting point with dicoms