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populse_logo

A project aimed to provide pipeline calculation tools to the neuroimaging community

capsul:

Python library to chain algorithms in pipelines

  • Encapsulate algorithms in Processes
  • Chain Processes within Pipelines
  • Execute pipelines in parallel with soma-workflow
  • Use a graphical interface to develop Pipelines
  • Configure one or more execution contexts
  • Embed Pipelines in any Python applications

mia_processes:

The official bricks library for populse_mia

mriconv:

MRI File Manager allows the reading of some raw and processed data files from MRI Spectrometers:

  • Bruker Paravision PV5 & PV6 (raw data of magnitude type)
  • Dicom from Bruker, Philips, Siemens
  • Philips Achieva (Par/Rec & Xml/Rec v4.2)
  • Nifti-1 (with or without Json)
  • Bids - Brain Imaging Data Structure

It also converts MRI images to Nifti-1:

  • Export MRI data in Nifti-1 format until 5 dimensions of the image (x, y, slice, frame, temporal)
  • Json files are created and associated with Nifti files in order to contain MRI parameters (see 'Irmage Json' page)
  • an option of anonymization allows to hide sensitive informations about the patient (name, age, sex, weight)
  • adaptation of orientation information in Nifti headers (tested on SPM, FSL)
  • option of customizing the Nifti file names
  • possibility to create text files containing bvecs & bvals for MRtrix and FSL (Bruker and Philips)

populse_db:

The database API of the populse project

populse_mia:

Multiparametric Image Analysis (populse_mia or MIA) is intended to be a complete image processing environment mainly targeted at the analysis and visualisation of large amounts of MRI data. In this environment, a process pipeline can be easily built by sequentially linking a succession of atomic computation (brick). Pipeline metadata as well as input, output or intermediate data are automatically managed by a database integrated into the environment. MIA is written in Python and is mainly based on populse's API, such as caspul, populse_db or soma_workflow.

soma-base:

Miscellaneous libs for the python environment of Populse / BrainVISA

soma-workflow:

A unified and simple interface to parallel computing resource

Parallel computing resources are now highly available: multiple core machines, clusters or grids. Soma-workflow is a unified and simple interface to parallel computing resources which aims at making easier the use of parallel resources by non expert users and software.