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LORIS MRI Release v20.0.0
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@MounaSafiHarab MounaSafiHarab released this 11 Aug 12:39
v20.0.0
7235a5c

This release of the Loris-MRI repo accompanies the LORIS 20.0 release.

New Features

Documentation

  • New: Complete documentation of LORIS-MRI setup, configuration, including scripts, tools, and database tables, and interaction with the LORIS front-end imaging modules. This documentation will be maintained up-to-date with each release to reflect the release codebase and features.

This documentation includes coverage of:

This release also includes:

  • A tool for auto-documentation of all LORIS-MRI perl scripts and libraries (mass_perldoc_md_creation.pl), designed to generate/update perldoc markdown files with each release #314

Other Features

  • Exclude specific scan types from database insertion as MINCs via a new setting in the LORIS Configuration module, under section: Imaging Pipeline (Existing projects -- see notes below for more information.) #319, #321

Improvements

  • comma-separated values (or ranges) are no longer permitted in the As a first step in the mri_protocol and mri_protocol_checks tables, as the first step in a multi-step process to normalize the protocol-related database tables.The insertion scripts will exit if they do #283, #318, & #327
  • As a first step in a multi-step process to normalize the protocol-related database tables, the mri_protocol and mri_protocol_checks tables no longer allow comma separated values. The insertion scripts will exit if they do #283, #318, & #327
  • no_nii configuration setting renamed to create_nii to make it more intuitive for users. This setting appears in the LORIS Configuration module, section: Imaging Pipeline (Existing projects -- see notes below for more information.) #294
  • Links to all scripts used in the insertion pipeline scripts have been moved to environment file variables #320
  • Improved logic in MRI.pm:getPSC()-- CenterID is returned first from the session table if possible, before regex matching in thePatientName` field. #317
  • No more jiv files generated by the insertion scripts. (Formerly, these files were used for BrainBrowser visualization, which also supports MINC) #310
  • Bug fix in the removal of the trailing / in the $data_dir path variable found in DTIPrep_pipeline, DTIPrepRegister and database_files_update.pl #307
  • No more warning about uninitialized value $oldCount when running tarchiveLoader #329
  • Removal of the extra unnecessary parameter that was passed to validateCandidate in the MRIProcessingUtility.pm #316

Notes for Existing Projects

  • To generate or viewperldoc documentation for scripts - please install the following dependencies:
     sudo -S cpan install Pod::Perldoc
     sudo -S cpan install Pod::Markdown
     sudo -S cpan install Pod::Usage

After installing these dependencies, use the perldoc feature to view documented scripts in a terminal, and/or generate documentation using pod2markdown #315

  • jiv file generation is no longer supported in the insertion pipeline. No action is necessary to be taken by existing projects. However, projects that wish to remove the jiv-related entries from their parameter_file table and move their jiv directory into the archive/ path can run the following script remove_jiv_data_from_db_and_filesystem.pl in the MRI tools/ directory. jiv files can be deleted if desired. #310

  • Projects should modify their environment file to include /data/%PROJECT%/bin/mri/uploadNeuroDB/bin in the export PATH line. (%PROJECT% should be replaced by your own directory name.) #320

  • Projects can now choose to customize the acquisition series they would like excluded from the DICOM-to-MINC conversion and protocol verification steps (limited and hard-coded to localizers up until this release). Case-insensitive regular expression matching is performed on the Series Description fields as customized by the project in the excluded_series_description accessible from the LORIS Configuration Imaging Pipeline section #319, #321

  • The mri_protocol and mri_protocol_checks tables no longer allow comma separated values. The insertion scripts will exit if they do (#283, #318). A LORIS script is provided with this release on the LORIS side to migrate comma-separated values (aces/Loris#3523).

  • Note that running the 20.0 LORIS release patch will rename your Config setting no_nii to create_nii, and will update your value for this setting (0/1) automatically. (#294)

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