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LORIS Modules

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christinerogers edited this page Mar 11, 2015 · 25 revisions

HOME > SETUP > LORIS MODULES

Modules are added and activated via the LorisMenu table. User permissions for viewing and accessing menus and menu items are stored in the LorisMenuPermissions table. For example, the Configuration module is visible under the Admin menu only to users who have config permission.

Document Repository

The Document Repository enables users to upload and organize project files of any type that can easily be viewable for users with appropriate permissions. Give full permissions to store documents on server:

chmod 777 /var/www/$projectname/modules/document_repository/user_uploads

A mail server will be required for sending out email notifications about Document Repository updates. In addition, in the Configuration Module under the "WWW" settings section, "Main LORIS URL" must be set. Also see more information on configuring Apache's file upload size limit.

Statistics

Includes tab delineated customizable Summary data, Demographics, Behavioural & Imaging data and Reliability rate. MySQL queries can be customized for project-specific batteries by editing php code. For example, to configure list of instruments for Behavioural statistics, copy NDB_Menu_statistics_site.class.inc from modules/statistics/php/libraries to project/libraries, and populate "var $instruments = array(...)" with instrument names.

Bug Tracker for LORIS and Imaging QC

LORIS installations are typically accompanied by the installation of bug tracker software such as Mantis, to facilitate discussion and resolution of instrument development and data entry issues, as well as Imaging QC.

Double Data Entry (DDE) and Conflict Resolver module

To enable specific DDE instruments, add at least 2 instruments within the "Study variables" section of Configuration Module. Once initial entry and DDE are complete, conflicts are resolved in the Conflict Resolver module, located under the 'Clinical' menu, accessible to front-end users by granting 'conflict_resolver' permission. Then timepoints with DDE instruments can be marked as 'Passed'.

Data Integrity Flag and Data Team Helper (Beta in 14.10)

The Data Integrity Flag and Data Team Helper modules are a powerful utilities for tracking workflow of data entry, data cleaning and validation for complete instrument datasets at any timepoint. In the Data Integrity Flag module, 5 status levels are used to indicate whether a dataset is (1) in progress for data entry, (2) complete and ready for cleaning, (3) checked and cleaned, (4) all behavioural feedback resolved, and finally (5) signed off by senior study staff.

Feedback module

The Feedback module allows users to flag and comment on any database field particularly for behavioural data entry. Two default feedback types exist: input and scoring errors. Additional feedback types can be added to feedback_bvl_type table.

Reliability module

This module enables review of consistency in clinical assessment, between examiners and across sites. Examiners can view and encode candidate behaviour from video, and the reliability module flags behaviour encodings which differ from the gold standard. Activate in loris/project/config.xml:

<ReliabilityInstruments>
    <Instrument>
        <Testname>aosi</Testname>
        <Threshold>0.5</Threshold>
        <Displayname>AOSI</Displayname>
    </Instrument>
</ReliabilityInstruments>

Data Dictionary Tool

Allows users to view/edit the Data Dictionary, which must first be created by running data_dictionary_builder.php script in tools directory.

Before running this script, ensure the parameter_type_category table contains a record where Type = 'Instrument'.

The input file automatically read by this script is called ip_output.txt - to create this file:

  1. For all PHP hand-coded instruments: run the quickform_parser.php script to generate ip_output.txt

  2. Append (cat) all linst files (for all active instruments built using instrument builder module) to ip_output.txt before running the data dictionary builder script.

Then run:

php data_dictionary_builder.php

Running this script is also a pre-requisite to loading the Data Query Tool.

Candidate Parameters

Candidate Parameter fields, displayed in the Candidate Information page, store data relevant to the candidate across all timepoints, such as race/ethnicity, co-morbidities, blood type, and IDs from other studies. Please see the Candidate Parameters wiki page for further instructions.

Candidate Information

All information regarding overall candidate, proband, participant status across timepoints including consent status is displayed in the front-end Candidate Information page, accessible via the "Edit Candidate Info" button. For more information, please see the Candidate Information wiki page.

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