VIP processing through Shanoir

Virtual Imaging Platform (VIP)

VIP (https://vip.creatis.insa-lyon.fr/) is a web portal for medical imaging applications. It allows access to scientific applications as a service, as well as distributed computing resources available in the biomed virtual organization of the EGI e-infrastructure.

Shanoir allow an authenticated user to process datasets on VIP platform pipelines. The resulting data is reintegrated into Shanoir as processed datasets.

How to

Prerequisite

To access VIP pipelines and start execution from Shanoir, the authenticated user must have previously created an account on the VIP platform.

This user must have the same email address than the Shanoir account, so that the two accounts can be linked between the two applications.

To create an account on VIP, see https://vip.creatis.insa-lyon.fr/sign-up.html.

Selecting dataset(s) to process

Datasets to process through VIP pipeline are selected through the Dataset search (Solr) view.

Once the selection made, click the Run a process button. Users must have admin rights on all the selected datasets.

Choosing a pipeline

Users can then select one of the VIP pipelines he has access to. They click Run this pipeline button to configure the pipeline execution.

Configuring execution

• Execution name is filled by default but can me modified by the user
• Group by allow users to define the level of dataset files grouping (by dataset, acquisition, examination) expected by the VIP pipeline.
• Dataset export format allow users to select the dataset export format (NIfTI or DICOM) expected by the VIP pipeline.

Other fields are execution parameters, specific to the chosen pipeline.

infile type fields correspond to the selected datasets. User can alter their selection by using regular expressions in these fields.

Once the execution started (after a few seconds), users are redirected to the Details on dataset processing view.

Following execution

Users can follow the state of the execution through the Jobs view.

In the Details on dataset processing view, they can check the status of the execution, and download some logs from VIP.

Accessing results

At the end of a successful execution, processings and processed datasets are created under each selected datasets.

The processings represents the VIP pipeline execution.

The processed dataset contains the raw results archive of the VIP execution, that can be downloaded through the Download process data button in the Details on dataset view

Some pipelines (e.g. ofsep_sequence_identification) can trigger specifically developed post-processing.