LORIS 15.10.2

This minor release addresses issues in the 15.10.1 release:

• Updated script for loading demographic data in Data Query Tool to handle new Subproject and Project configuration settings (fix)
• Removed third party script loading, introduced in 15.10 (fix)
• Updated embedded BrainBrowser to the recent v2.4.0 release, to correct for an inconsistency in display convention, where images may have appeared flipped (Left-Right) depending on imaging modality or acquisition type, due to mixing neurological/radiological display conventions (fix)
• Fixed bug where BrainBrowser was not correctly displaying 4 dimensional images (fix)
• Updated version number

Full list of changes since 15.10.1
If upgrading from a previous release, please also read Release notes from both 15.10 and 15.10.1 for additional details, caveats, known issues, and instructions for existing projects.

Known Issues

BrainBrowser 2.4.0 issues applicable to LORIS:

• gray scale mapping input file - fix here
• not compatible with mobile devices
• plane de-synchronization

LORIS 15.10.1

This minor release addresses two issues in the 15.10 release:

• Conflict Resolver not recording new data entry conflicts (fix)
• Search keyword filter impacting other unrelated modules (fix)

Full list of changes since 15.10
If upgrading from a previous release, please also read 15.10 Release notes for additional details, caveats, known issues, and instructions for existing projects.

Known Issues

• BrainBrowser viewer (embedded in Imaging Browser module) may flip images (Left-Right) due to mixing neurological/radiological display conventions. This display difference may appear between images acquired within the same scanning session for a given subject, perhaps depending on imaging modality or acquisition type. BrainBrowser's recent v2.4.0 release corrects this inconsistency in the display convention, and will be incorporated in LORIS 16.04.

LORIS 15.10

Fall 2015 release of LORIS : Full list of changes

Install process

• Install script enables setup when MySQL is hosted on a different machine than Loris
• For Mac install, see Mac Readme guidelines last updated for 15.04
• Apache configurations include setting AllowOverride All to accommodate Rewrite rules
• Smarty 3 is installed by Composer and does not require prior installation (since 15.04)
• new Wiki page on running the install script

Improvements and Documentation

• Re-designed Behavioural Feedback and Data Team Helper modules
• Subprojects and Projects can be created and managed via the front-end Configuration module. Recruitment targets can now be set at the Subproject level.
• One-click Data View Download to CSV format file in Access Profiles page (Candidate List)
• In User Accounts, when changing a user's permission settings, there is a new option to send a notification email to other site supervisors/coordinators (personnel selected from a list)
• MRI Header information now included in Excel dumps
• Direct links from Behavioural pages to Imaging datasets
• Dockerfile added
• API support
• Version file

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Imaging projects also see Loris-MRI Release Notes for Existing Projects for 15.10
• HTML will be displayed in console box upon first loading your upgraded Loris. Refresh your browser and/or delete the smarty/templates_c/ directory content to resolve.
• Subprojects (cohorts) and Projects are now managed in the front-end Configuration module. Run the import_projects.php script (located in modules/configuration/tools/) to migrate your subproject and projects settings from project/config.xml into the Config table. Then manually clean your config.xml file.
• Several Imaging Feedback categories have changed
• Apache configuration should enable Rewrite rules by setting AllowOverride All
  • Ubuntu apache config file: /etc/apache2/sites-available/$projectname.conf
  • CentOS apache config file: /etc/httpd/conf.d/apache-site.conf

Known Issues / Caveats

• Conflict Resolver does not record new data entry conflicts. Run the tools/detect_conflicts.php script on a frequent basis (e.g. by cronjob) to detect and report new conflicts. (Fix for 16.04)
• Beta features: Imaging Uploader AutoLaunch and Server Processes Manager module may require schema and code modifications
• Statistics module queries and calculations should be customized per project
• Form Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used
• Projects started before October 2014 who are missing the 'edit_final_radiological_review' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('edit_final_radiological_review','Can edit final radiological reviews','2');

• Document Repository is missing from the Tools menu. To display this menu item, run:

SELECT m.ID, p.PermID FROM permissions p CROSS JOIN LorisMenu m WHERE p.code='document_repository_view' AND m.Label='Document Repository';

LORIS 15.10 (Release Candidate 5)

• Fixed bug where non-study sites were appearing in the statistics module

LORIS 15.10 (Release Candidate 4)

• Fixed bug with validation errors not showing up in imaging_uploader
• Fixed bug where page links were not showing up in imaging_uploader

LORIS 15.10 (Release Candidate 3)

• Fixed various bugs in mri violations module
• Fixed issue with certification module not restricting data entry in instruments
• Removed an inefficient query from the statistics module which could cause large datasets to timeout.

LORIS 15.10 (Release Candidate 2)

• Fixed Dashboard loading problem where Project tag was enabled
• Fixed menu template for Survey Accounts

LORIS 15.10 (Release Candidate 1)

Fall 2015 release of LORIS : Full list of changes

Install process

• Install script enables setup when MySQL is hosted on a different machine than Loris
• For Mac install, see Mac Readme guidelines last updated for 15.04
• Apache configurations include setting AllowOverride All to accommodate Rewrite rules
• Smarty 3 is installed by Composer and does not require prior installation (since 15.04)
• new Wiki page on running the install script

Improvements and Documentation

• Re-designed Behavioural Feedback and Data Team Helper modules
• Subprojects and Projects can be created and managed via the front-end Configuration module. Recruitment targets can now be set at the Subproject level.
• One-click Data View Download to CSV format file in Access Profiles page (Candidate List)
• In User Accounts, when changing a user's permission settings, there is a new option to send a notification email to other site supervisors/coordinators (personnel selected from a list)
• MRI Header information now included in Excel dumps
• Direct links from Behavioural pages to Imaging datasets
• Dockerfile added
• API support
• Version file

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Imaging projects also see Loris-MRI Release Notes for Existing Projects for 15.10
• HTML will be displayed in console box upon first loading your upgraded Loris. Refresh your browser and/or delete the smarty/templates_c/ directory content to resolve.
• Subprojects (cohorts) and Projects are now managed in the front-end Configuration module. Run the import_projects.php script (located in modules/configuration/tools/) to migrate your subproject and projects settings from project/config.xml into the Config table. Then manually clean your config.xml file.
• Several Imaging Feedback categories have changed
• Apache configuration should enable Rewrite rules by setting AllowOverride All
  • Ubuntu apache config file: /etc/apache2/sites-available/$projectname.conf
  • CentOS apache config file: /etc/httpd/conf.d/apache-site.conf

Known Issues / Caveats

• Statistics module queries and calculations should be customized per project
• Form Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used
• Projects started before October 2014 who are missing the 'edit_final_radiological_review' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('edit_final_radiological_review','Can edit final radiological reviews','2');

• Document Repository is missing from the Tools menu. To display this menu item, run:

SELECT m.ID, p.PermID FROM permissions p CROSS JOIN LorisMenu m WHERE p.code='document_repository_view' AND m.Label='Document Repository';

LORIS 15.04

Spring 2015 release of LORIS : Full list of changes

Install process

• CentOS install support added to install script
• Updated Mac install Readme for Yosemite

Improvements and Documentation

• Composer dependency manager
• New project/data directory for project-specific data uploads
• More strict error handling for permissions and configuration settings
• Improved password hashing (with PHP 5.5+)
• Basic unit tests for every module
• New LorisForm class to replace HTML_QuickForm
• New Server Process Manager module for monitoring large data processes
• New Genomic Browser module
• New Training module for examiner certification
• Examiner module re-designed
• New Imaging Uploader module, including phantom handling
• Sample ranges provided for MRI protocol parameter checks
• Statistics module improvements
• Document Repository improvements
• Instrument Manager improvements
• Imaging Browser GUI enhancements

Notes for Existing Projects

Note all Caveats for existing projects, update your admin user account with all new/available permissions, and apply the Release patch

• Install Composer
• Configuration settings found in project/config.xml take precedence over Configuration module settings;
  it is recommended to remove any duplicate/overlapping settings from the config.xml file
• Config settings to be added to project/config.xml: HeaderTable, instrumentPermissions, multiSiteEnabledCenters
• New project/data directory recommended
• Access Profiles page hides Open Profile dialog for users with permission to view candidate data from multiple sites
• Retiring file extension *.super_sql for tables generated from .linst files; all MySQL files now just *.sql
• Please see the LORIS-MRI repository and wiki for details about our new web-based imaging uploader

Known Issues / Caveats

• localhost installations (e.g. on Mac) may encounter partial reduplication in URL path (More info:1173)
• isError() calls should be removed e.g. in php instrument files; error-checking now handled by base classes
• Numeric fields in forms created via the Instrument Builder will store a default value of 0 if not completed or if marked not_answered
• Statistics module queries and calculations should be customized per project
• Rules in the Instrument Builder are in beta
• Data Querying Tool data import scripts should be adapted if Consent feature is not used in Loris
• Projects started since January 2014 without a caveat_options table should run:

CREATE TABLE caveat_options (ID INT, Description varchar(255), PRIMARY KEY (ID));

• Projects started since September 2014 missing the 'mri_upload' permission should run:

INSERT INTO permissions (code, description, categoryID) VALUES ('mri_upload','MRI Uploader','2');

Loris 14.12.1

This minor release addresses bugs found in scripts in the 14.12 release which prevented some scripts from running properly.

Bug Fixes

Scripts from tools/ directory affected by this release:

• generate_tables_sql_and_testNames.php
• generate_tables_sql.php
• quickform_parser.php,
• data_dictionary_builder.php
• generic_includes.php (resolves issues with CouchDB import scripts, excelDump, and various others)

Click here for a full list of changes