Metadata-Version: 2.1
Name: pipetography
Version: 0.2.9
Summary: Pre/Post-processing pipeline for tractography wrapped around nipype and mrtrix3
Home-page: https://github.com/axiezai/pipetography
Author: Xi He Xie
Author-email: axiezai@gmail.com
License: Apache Software License 2.0
Description: # Pipetography
        > Nipype and mrtrix3 based pre-/post- processing pipeline for brain diffusion-MRI and generation of structural connectomes of the brain.
        
        
        ![CI](https://github.com/axiezai/pipetography/workflows/CI/badge.svg)
        ![docker](https://img.shields.io/docker/v/axiezai/pipetography)
        
        This repo currently only has pre-processing capabilities! More will be added in the near future.
        
        The pre-processing workflow has been updated to reflect what's seen in the optimal [DESIGNER pipeline](http://www.sciencedirect.com/science/article/pii/S1053811918306827) and on [mrtrix3 cloud apps on brainlife.io](https://brainlife.io). 
        
        ## Install
        
        Since most usages will be on HPC resources, I <em>highly recommend</em> that you use the `Singularity` or `Docker` recipe in the repository instead of installing the Python module.
        
        #### Singularity:
        
         - Currently has pathing issues as seen in the singularity issues page: https://github.com/hpcng/singularity/issues/5040, the 3.6 release candidate should fix this... For now, use docker image if you can. If not, the singularity container will not be able to execute freesurfer `recon-all` step of the workflow. All DWI preprocessing steps will work though.
         
         - Obtain the singularity image with `singularity pull docker://axiezai/pipetography:0.2.8` or `singularity build --remote pipetography.sif docker://axiezai/pipetography:0.2.8`. The second option allows you to build remotely via Syslabs Cloud, this will require a remote log tokeen in which you can obtain after registering at https://cloud.sylabs.io/builder. 
         
        #### Docker:
        
         - Pull the docker image: `docker pull axiezai/pipetography:0.2.8`
         
         - Run with BIDS directory and interactive bash terminal: `docker run -v <BIDS_DIR>:<Docker_BIDS_DIR> -it axiezai/pipetography:0.2.8 bash`
        
        Known container issues:
         - Singularity image missing freesurfer path to `nu_correct` as part of `$PATH`. 
        
         - If `singularity build` fails with `apt-get install` error complaining about unauthenticated packages, add `--allow-unauthenticated` to every `apt-get` line in the `sinngularity.def` file.
         
         - [Freesurfer6.0.0-min `recon-all` is missing commands if `-parallel` or `-openmp` are set to `True`](https://github.com/ReproNim/neurodocker/issues/285). The default `-parallel` **setting has been set to False for `pipetography.pipeline`**.
         
        #### Creating your own environment and install `pipetography` as a Python module:
        
        `pip install pipetography`
        
        Since `pipetography` is a `Nipype` wrapper around `mrtrix3`, `ANTs`, and `FSL`, you have to follow their installation instructions and set them up appropriately on your machine as well:    
         - [mrtrix3 v3.0.0](https://mrtrix.readthedocs.io/en/latest/installation/before_install.html)
         
         - [ANTs](https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS)
             
         - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
         
         - [Freesurfer v6.0](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
         
         - [Matlab Run Time Compiler for freesurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime)
         
        
        ## The pipeline:
        
        Currently supports `-rpe_none`  and `-rpe_all` options.
        
Keywords: diffusion-mri,tractography,neuroimaging,nipype
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
