Skip to content

LORIS MRI Release v20.2.0
Compare
Choose a tag to compare
@cmadjar cmadjar released this 01 Feb 20:43
v20.2.0
18fd6d2
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

This release of the LORIS-MRI repository accompanies the LORIS 20.2.0 release.

New Features

  • EEG BIDS import pipeline scripts, written in python (#337, #347)

  • Allow insertion of MINC files without associated DICOM files, or TarchiveID or UploadID values (#340): as of this release, it is possible to insert directly MINC files into the database without associated DICOM files using minc_insertion.pl directly.

  • New generic (non-MINC) file image insertion script (#271): this script allows insertion of any non-MINC file image into the database via the script imaging_non_minc_insertion.pl to insert non-MINC files into the files table.

  • New tool to select, extract and tar DICOM files for a specified regex matching the PatientName and/or acquisition protocol (#360)

  • Added a check for the SeriesUID/echo_time pair before insertion into the database to avoid duplication of files in the database. If a file is already registered in the database with that same SeriesUID/echo_time pair of values, the insertion script will return a message saying the image is already inserted in the database with the name of the registered file (see #359 for more details)

Improvements

  • Non DICOM files are now ignored when running the default imaging insertion (MRI) pipeline (see #371 and #373)

  • Fixed a bug where a DICOM without the header field (0020,0032) was automatically excluded by get_dicom_info.pl because if was flagged as non-DICOM. With this update, running this script with the option -slicepos (#365) will include and load DICOMs that do not contain this header field.

  • New Configuration module field under the Imaging pipeline section called "Modalities on which SNR should be calculated (compute_snr_modalities)". This replaces the getSNRModalities() function in the prod (profile configuration) file (#358)

  • Fixed a bug when running the DTIPrep pipeline on datasets where NIfTI files are created at the time of insertion (before the bug fix, if the T1W file selected was the NIfTI file instead of the MINC file, then the MINC tools would fail running and the DTIPrep pipeline crashed; this has been fixed in #355).

  • Fixed an error message that was displayed in the terminal when loading NeuroDB/MRI.pm library (#357)

  • Uses perl function getpwuid instead of whoami fetch the Linux User ID (#368)

  • Documentation for more perl scripts: dicomSummary.pl (#342) and get_dicom_info.pl (#343)

  • Fixed cleanupTarchives.pl tool and documented it (#344)

  • Fixed updateHeaders.pl tool and documented it (#345)

Notes for Existing Projects

  • Important: Update your Configuration module, Imaging section -- New field: "Modalities on which SNR should be calculated (compute_snr_modalities)" AND remove from your prod file the function called getSNRModalities() (see #358)

  • To use the EEG BIDS pipeline, simply follow the install instructions in #337, #347. For detailed information, consult the updated README.md and 02-Install.md under docs/

  • To use the new generic (non-MINC) file image insertion script (#271), you will need to install the JSON CPAN library (may require sudo) :

cpan install JSON
Assets 2