gmri2fem 0.2.8

Processing pipeline for glymphatic MRI.

gMRI2FEM

gmri2fem is a python package for processing of human glymphatic MRI-images, i.e. contrast-enhanced brain images, with special focus on concentration-estimation and conversion into dolfin for mathematical modelling of brain tracer transport using the finite element method. The data functionality was developed for the MRI processing workflow for the GRIP-project. The package both provide a library of useful functions as well as a CLI for processing different types of images.

Installation

Dependencies

gmri2fem has some python- and non-python dependencies which are not easily installable through pip:

• FreeSurfer
• greedy
• FEniCS
• SVMTK

Instructions for how to install these may be found on their websites. It is, however, possible to gmri2fem and run large portions of the pipeline whithout these dependencies. To install the python package gmri2fem, clone this repository and run

pip install . 

from the root directory. This will install the python packages and the CLI.

Example usage

For a rough documentation on how to use the various exposed CLI-commands, we recommend looking at the Snakefiles for the Gonzo data pipeline at (https://github.com/jorgenriseth/gonzo). The CLI has several levels of subcommands. To run the main entrypoint:

$ gmri2fem --help
Usage: gmri2fem [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  brainmeshing
  dcm2nii-ll
  dcm2nii-mixed
  dti
  i2m
  mri
  seg

MRI

Usage: gmri2fem mri [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  concentration
  hybrid-t1map
  looklocker-t1-postprocessing
  looklocker-t1map
  mixed-t1map
  reslice4d
  t1-to-r1
  t1w-normalize
  t1w-sigdiff

Example command:

Usage: gmri2fem mri looklocker-t1map [OPTIONS]

Options:
  --input PATH       [required]
  --timestamps PATH  [required]
  --output PATH      [required]
  --help             Show this message and exit.