LORIS-MRI Release v24.1.10

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Fix a bug when determining file run number for new uploads (#909)

LORIS-MRI Release v24.1.9

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Fix incomplete format bug when querying EchoNumber from the files table #889
• Add a check before inserting in mri_candidate_errors.py class #891, #902
• Fix bug when scan type is provided to run_nifti_insertion.py script #899
• Fix bug when scan type is not provided to run_nifti_insertion.py script #901
• Fix run numbering logic to use SessionID instead of TarchiveID to determine the list of files already inserted in the database for the session #903

Python BIDS import pipeline

• Rename Task to Property for new events database table support #900

Tool scripts

• Fix gzip_nifti_files.pl tool script message when failed to gzip a NIfTI file #898

LORIS-MRI Release v24.1.8

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Addition of a delete_file function for files present on an S3 bucket (#881)
• Fix NIfTI insertion bug that occurred when running the script with the --scantype option (#883)
• Fix bug where the same violation was duplicated in the mri_protocol_violated_scans or mri_violations_log tables (#884)

Python BIDS import pipeline

• Addition of a workaround for scipy known issue (in loadmat) to better support Matlab 7.3 HDF5 SET files (#880, #886)
• Support additional event fields (custom columns) that could be present in BIDS events.tsv files (#873)

Caveat for existing projects

• Make sure to install the mat73 python library using pip install mat73 after having source the LORIS-MRI environment file

LORIS-MRI Release v24.1.7 - INCLUDES CRITICAL BUG FIX INTRODUCED IN 24.0.0

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

• pull critical bug fix for 24.0 release regarding broken DICOM archive links (#872)
• fix bug when trying to write IntendedFor information in fieldmap JSON files already uploaded to S3 (#874)

LORIS-MRI Release v24.0.4 - CRITICAL BUG FIX FOR 24.0.0

This is a critical bug fix release for LORIS-MRI version 24.0. It resolves the following bug introduced in 24.0.0 where the DICOM archive links were not being updated in the database after they were being moved to the year subfolder, generating broken links in the DICOM archive module when trying to download the DICOM archives. (#872)

LORIS-MRI Release v24.1.6

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Ignore case when checking regex for series description in the python pipeline (#859)
• Add download from S3 and reupload to S3 if file provided to run_nifti_insertion.py is an S3 URL (#860)
• Fix IntendedFor bug when no acquisition time is available in JSON files (#861, #862, #867)
• Fix paths when there are no / at the end of paths specified in the Config module (#866)
• Properly update mri_upload 'Inserting' column when different sections of the pipeline are being run (#868)

LORIS-MRI Release v24.1.5

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Fix permission denied issue when trying to erase temporary directories after the pipeline is done running (#853)
• Fix two matching protocols' error when the matching protocols are actually referring to the same scan type (#856)
• Add missing Python exit codes that are already present on the Perl side (#857)

LORIS-MRI Release v24.1.4

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Fix the database query used to determine if a NIfTI file was already inserted in the files table with same SeriesUID, EchoTime, EchoNumber and PhaseEncodingDirection values (#845)
• Fix the logic to determine the run number of a NIfTI file when previously inserted files for the session have been pushed to S3 (#846)
• Raise error when the chunk creation subprocess fails instead of failing silently (#848)
• Revert chunk pb2 changes so that import statements work with old and new versions of the compiler/interpreter/core library (#849)

LORIS-MRI Release v24.1.3

This is a bug fix release for LORIS-MRI version 24.1. It resolves the following bugs:

Python dcm2bids insertion pipeline

• Fix NoneType errors happening when the visit of a scanning session does not exist in the database (#824)
• Fix NoneType errors when RepetitionTime or EchoTime has not present in the JSON side car file (#825)
• Fix run_nifti_insertion.py pipeline error when specifying a scan type with option -s to the script (#829)

Python push to S3 pipeline

• Add capability to download a file from the S3 bucket by adding a download_file function t the AwsS3 python class (#826)
• Modifies the upload_file function of the AwsS3 python class to be able to handle objects starting with s3://bucket_name/ the same way it is handled by the download_file function of the same class. (#827)
• Skip protocol violated scans not present anymore on the filesystem (#831)
• Change run_push_imaging_files_to_s3_pipeline.py permission to be executable (#830)
• Skip file paths starting with s3:// from the push to S3 since the file is already on the S3 bucket (#833, #834)

BIDS import pipeline

• Protocol Buffer files (python/react-series-data-viewer/protocol_buffers/) compiled with protobuf v3.20(#823)
• Default fallback when no site and project are provided in participants.tsv (#823)
• Reject events metadata that do not agree with the expected BIDS spec types (see: https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/05-task-events.html) (#823)

LORIS-MRI Release v24.1.2

This is a bug fix release for LORIS-MRI version 24.0. The release includes:

PET insertion pipeline fix

• pull the PET insertion pipeline fix that was released in 24.0.3

Python dcm2bids MRI insertion pipeline

• Remove hardcoded dcm2niix command call to use the value stored in the converter Config Setting instead (#815)