Package Recipe 'meta-neuro'

recipe meta-neuro

Medial Tractography Analysis (MeTA)

Homepage:: https://github.com/USC-LoBeS/meta
Developer docs:: https://github.com/bagari/meta
License:: BSD-3-Clause
Recipe:: /meta-neuro/meta.yaml

MeTA is a workflow implemented to minimize microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the bundle length in the voxel-space directly while effectively preserving bundle shape and efficiently capturing the regional variation within and along white matter (WM) bundles.

package meta-neuro¶

Versions:

2.0.1-0, 2.0.0-0, 1.0.1-0, 1.0.0-1, 1.0.0-0

Depends:

on dipy
on libgcc >=13
on libitk >=5.4.4,<5.5.0a0
on libitk-devel >=5.4.0,<5.5.0
on libstdcxx >=13
on libxml2
on libxml2-16 >=2.15.1
on nibabel
on numpy
on pandas
on pip
on python >=3.11,<3.12.0a0
on python_abi 3.11.* *_cp311
on pyvista
on qhull
on scipy >=1.15.0
on setuptools
on tqdm
on tslearn
on vtk >=9.4.1,<9.6
on vtk-base >=9.5.2,<9.5.3.0a0

Additional platforms:

osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install meta-neuro

to add into an existing workspace instead, run:

pixi add meta-neuro

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install meta-neuro

Alternatively, to install into a new environment, run:

conda create -n envname meta-neuro

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/meta-neuro:<tag>

(see meta-neuro/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/meta-neuro/README.html)