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Imaging Uploader

Purpose

The imaging uploader is intended to allow users to upload, browse, and track pipeline insertion progress.

Intended Users

The primary users are MRI technicians or site coordinators uploading imaging scans for registered LORIS candidates and timepoints.

Scope

The imaging uploader has the following built-in capabilities to facilitate timely scan insertion into the LORIS database. Specifically, it allows to browse uploaded scans using the Browse tab, upload imaging scans using the Upload tab, and track scan insertion status through the Progress column and a Log Viewer which displays in either Summary or Detailed mode relevant feedback messages about insertion success or failure causes.

Uploaded scans can be overwritten if insertion status is Not Started or Failed (i.e. if the Progress is neither In Progress nor Success).

NOT in scope:

The imaging uploader does NOT read the DICOM files within the uploaded scans. As such, it does not check if the files within the uploaded scan are of the expected DICOM type, nor whether the PatientName and/or PatientID DICOM headers are properly de-identified according to the LORIS convention. This check is however done as the first step on the LORIS-MRI side; i.e. as soon as the insertion pipeline is triggered.

Requirements

This module requires the use of another software package, LORIS-MRI. It consists of a series of scripts used for validation of image uploads.

For a successful upload:

  • The CandID must exist in the database
  • The PSCID must be valid for the CandID
  • The Visit label must be valid for the CandID
  • The candidate must be active in the database
  • The session must be active in the database
  • The uploaded file is expected to be of one of the following types: .tgz, .tar.gz or .zip.
  • The file should not exceed the max upload size
  • The filename should follow the: PSCID_CandID_VisitLabel_OptionalSuffix naming convention

Permissions

Module Permission

The imaging uploader module uses one permission called imaging_uploader that is necessary to have access to the module and gives the user the ability to upload and browse all scans uploaded to the database.

Filesystem Permission

The path on the filesystem where the uploaded file go (see section Database Configuration) should be readable and writable by the web server. This is automatically achieved by the LORIS-MRI install process.

Configurations

The imaging uploader has the following configurations that affect its usage:

LORIS-MRI

The imaging insertion pipelines and libraries in the Loris-MRI repo must be installed, configured, and tested before imaging data can be loaded into LORIS via this module. Please visit the documentation for LORIS-MRI for more information.

Install Configurations

To enable the Imaging Uploader to handle large files, please follow the instructons for Handling Large File Uploads.

Database Configurations

ImagingUploaderAutoLaunch - This setting determines whether the insertion pipeline that archives the scans is triggered automatically or manually.

MRIUploadIncomingPath - This setting determines where on the filesystem the uploader is to place the uploaded scan. Default location is /data/incoming/. This directory is created during the installation of LORIS-MRI. Note: Uploaded scans are erased from the MRIUploadIncomingPathfollowing a successful archival and insertion through the LORIS-MRI pipeline.

Interactions with LORIS

  • The TarchiveInfo column links to the DICOM Archive module for that scan
  • The Number of MincInserted column links to the Imaging Browser module for that candidate's session
  • The Number of MincCreated column links to the MRI Violated scans module if violated scans (i.e. scans that violate the MRI protocol as defined by the study) are present
  • If ImagingUploaderAutoLaunch configuration is enabled, the Server Process Manager under the Admin menu can be consulted for scans insertion progress (exit codes, error files, etc...).