LORIS-MRI Release v26.0.0

This release of the LORIS-MRI repository accompanies the LORIS 26.0.0 release

• List of all LORIS-MRI 26.0.0 changes (not including schema and module changes which were contributed to the main LORIS repo)
• Full Changelog: v25.0.0...v26.0.0

New Features

• Added HED Support and replaced annotations by EEG BIDS events by @jeffersoncasimir in #1041
• Use the CenterID instead of the CenterName to identify scans by @nicolasbrossard in #1043

Fixes

Install improvements

• Minor changes to the environment logic for the install by @laemtl in #1134
• Fix Blake2 PERL Module for earlier releases of Ubuntu by @laemtl in #1135 and #1136

Perl scripts improvements

• Properly set field TarchiveSeriesID for acquisitions that do not have an echo time when inserting data in tarchive_series by @nicolasbrossard in #1055
• Improve command line arguments validation of minc_insertion.pl by @nicolasbrossard in #1123
• Remove the extra constraint in register_processed_data.pl saying that the SourceFileID provided as an argument to the script should not be listed in InputFileIDs provided as an argument to the script by @cmadjar in #1097
• Fix ProjectID error triggered when running register_processed_data.pl by @cmadjar in #1103

Python dcm2niix scripts

• Fix NoneType error when S3 configs are not set properly by @cmadjar in #1110
• Fix NoneType error when running run_dicom_archive_validation.py on an inexistant UploadID by @cmadjar in #1111

BIDS import and EEG pipeline

• Bug fix in electrode insertion, where more than one electrode was being inserted every time by @jeffersoncasimir in #1017
• Added validSamples to index.json by @jeffersoncasimir in #1030
• Fixed typos preventing bids_import.py to run by @jeffersoncasimir in #1129
• Replaced instances of 'derivatives' with 'derivative' by @jeffersoncasimir in #1130
• Fix off-by-one error of mass_electrophysiology_chunking.py by @jeffersoncasimir in #1131

Tools

• Fixes segmentation fault error when running delete_imaging_upload.pl script by @nicolasbrossard #1121
• Fixes of the cronjob for PET uploads by @laemtl in #1113
• Fix JSON format produced by minc_to_bids_converter.pl by @CamilleBeau in #1127

New Contributors

• @CamilleBeau made their first contribution in #1127

Full Changelog: v25.0.0...v26.0.0

Notes for existing projects

If you plan to use the HED support we developed for the bids_import.py pipeline, make sure to run the PHP script on the LORIS side: https://github.com/aces/Loris/blob/main/tools/importers/insert_hed_schema.php

LORIS-MRI Release v24.1.16

This is a bug fix release for LORIS-MRI version 24.1 that includes the following fixes for the bids_import.py EEG pipeline:

• A few minor changes in the chunks script to fix warnings
• Add the .set path overrides logic to the extract_eeg_bids_archive.py script
• Disable the .set path overrides logic in bids_import.py in --no-copy is set to true.

LORIS-MRI Release v24.1.15

This is a bug fix release for LORIS-MRI version 24.1 that includes the following features:

• support for partial dataset ingestion in bids_import.py
• support in bids_import.py to ingest datasets without copying files in assembly_bids for cases where the datasets are already in assembly_bids
• new script ingest_eeg_bids_datasets.py to ingest all EEG uploads with status extracted

To import partial datasets:

python extract_eeg_bids_archive.py -p database_config.py
python bids_import.py -p database_config.py -d  /data/loris/data/assembly_bids/sub-<label>/ses-<label>/eeg --nobidsvalidation --type raw --nocopy

Notes: the --nocopy option is required for partial datasets since the process to create a copy in assembly_bids requires a dataset_description.json file.

bids_import.py new options:

• --nobidsvalidation: disable validation for datasets without a dataset_description.json (partial import). Required for partial ingestion.
• --nocopy: disable dataset copy in data assembly_bids
• --type: specify the dataset type for datasets without a dataset_description.json (partial import)

If you are going to use this pipeline, please contact us.

LORIS-MRI Release v24.1.14

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

• [Install] removal of the pyblake2 library from the pip requirements.txt file (#1038)
• [Python push to S3 script] add method to check and skip duplicate content uploads to S3 (#1037)
• [Python BIDS import and dcm2bids pipelines] Fixes for parameter_file value lists (#1025 and #1034)

Notes for existing projects using one of the python pipelines

If you have been any of the python pipeline to insert MRI data (bids_import.py or the dcm2bids pipeline) then, it is very likely that some of the list were improperly saved in parameter_file. To that end, we create a script to correct the incorrectly saved list values. The following command can be run from the root directory of the LORIS-MRI code:

python tools/correct_lists_incorrectly_saved_in_parameter_file.py -p database_config.py

Note: this is not necessary if you have been only using the perl dcm2mnc insertion pipeline in your project.

LORIS-MRI Release v24.1.13

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

• AWS upload subdirectory fix for EEG extraction script (#1023)

LORIS-MRI Release v24.1.12

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

• modification of extract_eeg_bids_archive.py's permission to be executable (#1018)
• add a functionality to copy AWS S3 objects within buckets (#1016, #1019)

LORIS-MRI Release v25.0.0

This release of the LORIS-MRI repository accompanies the LORIS 25.0.0 release.

• List of all LORIS-MRI 25.0.0 changes (not including schema and module changes which were contributed to the main LORIS repo)
• Full Changelog: v24.1.11...v25.0.0

New Features

• [EEG-BIDS] Add support for events.json file & HED Tags (#769, #968)
• [dcm2bids] Add support for images that do not have a series description (#778)
• [EEG-BIDS] Electrode coordinate systems (#885, #908)

Bug fixes

• HRRT PET install documentation (#813)
• Updated rules to set the default project, cohort (#809, aces/Loris#8384)
• Refactor remaining array configs to use ConfigOB instead of the DBI library (#770)
• [Perl pipeline] Do not duplicate violation entry if it already exists (#896)
• Chunking - add _get_info missing parameter (#958)
• [bids_imports] Fix derivative annotation files copied over to raw folders (#776)
• [petupload_cron_prod] Automatically create dirs (#966)
• [imaging_non_minc_insertion] Log execution date (#985)
• [imaging_non_minc_insertion] Error message obtained when an invalid upload ID is specified on the command line (#984)
• [minc_to_bids_converter.pl] BIDS validator: Fix authors array (#1003)
• [register_processed_data] Report Project ID missing when it really is (#987)
• Add ProjectID to scanner candidate (#914)
• Enforce use of -uploadID in script uploadNeuro/tarchive_validation.pl (#974)
• Change mkdir to make_path in run_defacing_script.pl (#978)
• [register_processed_data] Add more validation for options -sourceFileID and -inputFileIDs (#999)
• [imaging_non_minc_insertion] Validate -date_acquired argument (#1002)
• [dicomSummary] Improve option behaviour and use sdiff instead of tkdiff for differences (#1000)
• [get_dicom_files] fix -id parameter (#995)
• Control DB parameters initialization (#991)

Documentation

• Fix MriScanner::determine_scanner_information description (#993)
• Fix documentation of replicate raisinbread for MCIN dev tool (#976)
• Addition of a PET import tool example for BIC PET transfers (#840)

Notable SQL changes

Note that the Subproject table has been renamed Cohort in LORIS v25.0.0 (#882, aces/Loris#7817)

Notable non-SQL changes

• Running batch scripts under tools/ directory with QSUB may fail on Ubuntu 22. To fix this, turn off the is_qsub configuration by setting the Project batch management used config to 'No' under the Imaging Pipeline tab of the Configuration module.

LORIS-MRI Release v24.1.11

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

General python code fixes

• fix blake2b and md5 hashing algorithm used to generate files' hashes stored in the database (#916)

Python dcm2bids insertion pipeline

• print proper error message when running dicom_archive_validation.py on an UploadID that does not exist in the database (#962)
• print proper error message when running dicom_archive_validation.py on an improper UploadID/ArchiveLocation combination (A.K.A. the ArchiveLocation is not linked to the UploadID provided as input to the script and vice versa) (#963)
• fix handling of options provided to the script run_push_imaging_files_to_s3_pipeline .py (#964)
• better handle bad configuration of S3 in database_config.py and Config module (#965)

BIDS import pipeline

• add support for using CandID in the BIDS subject's IDs that is imported (#912)
• add CandID/PSCID validation in the folder name if the flag -i is used when importing BIDS data (#912)

New script

• addition of a script that will extract an electrophysiology upload in the assembly_bids directory alongside the MRI data imported by the dcm2bids pipeline (#970)

Caveat for existing projects

• Since the hashes were not created properly by the python pipelines (A.K.A. bids_import.py and dcm2bids pipelines), the hashes stored in the database are incorrect and need to be corrected. In order to do that, a script has been made available in the tools directory. To correct all the incorrect MD5 and BLAKE2b hashes, run the following command:

python tools/correct_blake2b_and_md5_hashes_in_database.py -p database_config.py

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