XNAT Pipeline-engine is a Java-based workflow framework nicely integrated (that's basically its inception purpose) in XNAT. Pipeline-engine uses XML-based workflow definitions for processing data hosted in XNAT by linking sequential activities or steps.

• Provides mechanisms for batch-mode triggering pipeline instances (via REST API).
• Enables submission of jobs to a Distributed Resource Management (DRM) system supporting the Distributed Resource Management Application API (DRMAA) specification, e.g. SGE.

XNAT pipelines repository, see the wishlist for incomming apps.

• ExamCard extractor :: Extracts Philips ExamCard objects embedded in DICOM object files
• FreeSurfer :: FreeSurfer recon-all pipeline with XNAT assessor output with stats metrics
• mricron :: DICOM and PARREC flavoured pipelines for imaging data conversion to NIFTI format (using dcm2nii)
• Quality Assessment Protocol :: QA analysis on functional/structural MRI data
• mricrogl :: New generation of DICOM-to-NIFTI format conversion pipeline (using dcm2niix)
• DTI-preprocessing :: Compute preprocessing corrections on MRI DTI scans
• MRI bias field correction :: correcting intensity non-uniformity (i.e. bias fields)
• MRI anatomical defacer :: Automated facial traits removal (defacing) of anatomical scan data.
• qMRI :: Calculate quantitative anatomical MRI (qMRI) mapping. qMRI provides MRI measures that are comparable across sites and time points. More background here.

Jordi Huguet, Department of Neuroradiology & Brain Imaging Centre, AMC-UvA Amsterdam

This work is licensed under the terms of the GNU GPLv3 license.