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LORIS MRI Release v21.0.0
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@cmadjar cmadjar released this 01 Aug 13:58
· 2 commits to 21.0-dev since this release
v21.0.0
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Learn about vigilant mode.

This release of the LORIS-MRI repository accompanies the LORIS 21.0.0 release.

New Features

  • Replaced Gender field with Sex in the candidate and tarchive tables (see #336, #382)

  • New script to Delete uploaded scans (see #391 ), in the tools directory

  • New script to generate BIDS-compliant structures for existing NiFTi files stored in your LORIS instance - tools/MakeNiiFilesBIDSCompliant.pl (see #198)

  • Added the image_type header into the mri_protocol table for protocol discrimination of acquisitions. This header is particularly useful to differentiate phase and magnitude files of fieldmap acquisitions (the only difference between the two image types is in the image_type header) (see #416)

  • Addition of a tool that produces 3D rendering of the face for visual QC of defaced images (see #415)

  • Added a batch script to run defacing in parallel on multiple CPUs using QSUB if the Config Setting is_qsub is set (see #414)

  • Grep the age of a candidate at the time of acquisition from the BIDS sub-XXX_scans.tsv file and insert it into physiological_parameter_file (see #447)

Improvements

  • Cleaned up multiple database paths referring to the same path (see #399)

  • Replaced CenterID field of the candidate table by RegistrationCenterID (see #341, #442)

  • Refactoring of database calls using Moose (see #282, #295, #303, #311, #330)

  • Replaced all hardcoded prod file mentions with (pre-existing) Config setting (see #254)

  • Removed the unused column PendingStaging from the files table (see #292 and LORIS patch aces/Loris#3569)

  • Updated the exit code of updateMRI_Upload.pl to use the ExitCode.pm (see #305)

  • Harmonized the multiple ways of getting MINC header information in the code (see #351)

  • Added missing CPAN dependencies in the install script of LORIS-MRI (see #439)

  • Reordering of the environment file for new installs (see #148)

  • Upgraded the BIDS insertion pipeline to use the more recent version of pybids (0.9.1) (see #448)

Notes for Existing Projects

Make sure to run the release patch on the LORIS side as there are significant SQL changes affecting the MRI side of LORIS.
Many core Loris-MRI scripts have now been updated with improved command-line arguments (see notes below.)

  • Caveat for custom tools: replace Gender with Sex when querying the candidate or tarchive table

  • Caveat for custom tools: replace CenterID with RegistrationCenterID when querying the candidate table

  • Note Config path changes: Cleaned up multiple database paths referring to the same path (see #399)

  • Make sure that your Config setting dataDirBasepath is configured to the proper data path (typically /data/%PROJECT%/data)

  • Caveat for projects using the BIDS insertion pipeline. Since pybids changed the way files are queried in the most recent versions, the insertion LORIS-MRI BIDS insertion pipeline had to be refactored to work with the latest stable version of pybids (0.9.1). To upgrade your install of pybids, simply run in your python virtualenv (a.k.a. after having sourced your virtualenv: source $LORIS_MRI/python_virtualenvs/loris-mri-python):

pip uninstall pybids
pip install --upgrade pip
pip install pybids==0.9.1
  • New CPAN dependencies to install:
sudo cpan install Moose
sudo cpan install MooseX::Privacy
sudo cpan install TryCatch
sudo cpan install Throwable

  • Projects that plan on using the defacing scripts should reorder their environment files as shown in PR #429.

  • The following scripts must now be run with the -profile <filename> option set (filename typically prod)

    • batch_upload_tarchive.pl
    • tools/seriesuid2fileid.pl

  • Projects that call one of the following scripts using a cronjob should update their cronjob to add the .pl extension to the script:

    • batch_uploads_imageuploader => batch_uploads_imageuploader.pl
    • batch_uploads_tarchive => batch_uploads_tarchive.pl
    • tarchiveLoader => tarchiveLoader.pl
    • uploadNeuroDB/bin/Mincinfo_wrapper => uploadNeuroDB/bin/Mincinfo_wrapper.pl
    • uploadNeuroDB/bin/mincpik => uploadNeuroDB/bin/mincpik.pl
    • tools/seriesuid2fileid => tools/seriesuid2fileid.pl

  • Before running the deletion script on an old upload (data uploaded before release 20.3), make sure that the script called cleanup_paths_of_violation_tables.pl (in the tools directory) from #403 (release 20.3) has been run to update all paths in mri_violations_log, mri_protocol_violated_scans and MRICandidateErrors to their actual path in the trashbin subdirectory of your LORIS-MRI data directory.

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