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.