LORIS-MRI Release v26.0.4

This is a bug fix release for LORIS-MRI version 26.0 that includes the following fixes:

• fix various little bugs preventing the insertion of a MINC file without DICOMs #1290
• fix call to plotting function of nilearn to work with latest release of the nilearn package #1316

LORIS-MRI Release v27.0.0

This release of the LORIS-MRI repository accompanies the LORIS 27.0.0 release

• List of all LORIS-MRI 27.0.0 changes (not including schema and module changes which were contributed to the main LORIS repo)
• Full Changelog: v26.0.0...v27.0.0

New Features

New DICOM study importer developed in Python

• Creation of a new DICOM study importer developed in Python that supports Enhanced DICOMs (import_dicom_study.py) #1117, #1264, #1278

Refactoring

• ORM Implementation in the python scripts #1152, #1192, #1200, #1207, #1214, #1216, #1217, #1221, #1224, #1229, #1232, #1249, #1255, #1270, #1271
• Candidate ID SQL refactoring #1252, #1291, #1285, #1286, #1248
• Scan type SQL refactoring #1139
• Creation of a new lib.config module #1253
• Creation of a new lib.util python module #1238
• Creation of a new lib.util.crypto module to compute file hashes #1263
• Migrate remove_empty_directories to lib.util.fs (file sytem operation module) #1265
• Refactor of the get_subject_info function of python configuration file #1146, #1150, #1190, #1231, #1250
• Refactor logging architecture in lib.logging #1191
• Modify the way credentials are obtained for mysqldump in delete_imaging_upload.pl script #1282
• Move python scripts to python/scripts #1196

Various tests and code sniffer implementation

• Typing and code sniffer implementation #1167, #1170, #1172, #1149, #1192, #1193, #1194, #1197, #1210, #1218, #1251, #1237
• Docker setup for LORIS-MRI integration tests #1138, #1171, #1173, #1179, #1187, #1195, #1202, #1215
• Add integration tests for:
  • run_dicom_archive_loader.py #1203, #1247
  • run_dicom_archive_validation.py #1242
  • mass_nifti_pic.py #1274
  • run_nifti_insertion.py #1257
  • import_dicom_study.py #1262, #1266
  • checking the ORM definitions against the LORIS SQL #1198
• Add database unit tests #1188

Bug fixes

• Fix incorrect uses of re.match #1294
• Fix bugs preventing the insertion of a MINC file not derived from a LORIS DICOM archive #1289
• Fix SQL statement in MRI.pm #1284
• Fix compilation error in uploadNeuroDB/NeuroDB/ImagingUpload.pm #1283
• Fix perl dependencies #1205
• Fix copy path for root-level events.json #1276
• Fix ingest_eeg_bids_datasets.py #1275
• Add Date::Parse to the set of required Perl libraries #1269
• Fix large file hashing memory consumption #1236
• Fix install script and update python installation #1145, #1234
• Improve Python requirements order #1222
• Fix [ERRNO: 18] Incorrect link accross file systems... error triggered in BasePipeline.move_file #1168
• Add leading r for literal regexes across the python code #1176

New Contributors

• @kongtiaowang made their first contribution in #1138

Notes for existing projects

• Update to python requirements: Need to upgrade python to version 3.11 or higher for the python code to work See LORIS PR #1145
• Refactoring of the candidate ID structure on the SQL side might impact queries in project-specific code. See LORIS PR #9556 SQL patch
• Refactoring of the Scan type field names across the MRI tables might impact queries in project-specific code. See LORIS PR #9304 SQL patch
• New ORM implementation and deprecation notices: moving python code to use ORM instead of direct SQL queries. Old functions implementing direct SQL queries will generate deprecation notices so that projects can start moving toward the use of ORM instead of direct queries in the python code. Direct querying will be slowly phased out from the LORIS-MRI code but functionality should be compatible with 26.0 for now.
• Significant changes to the python database_config.py file has been implemented in this release. Please, check the latest template for this file to upgrade your config file accordingly
• Python scripts have been moved under python/scripts. You will need to make sure that /opt/{PROJECT}/bin/mri/python/scripts are added to the PATH environment variable in your environment file
• There is a new DICOM study importer developed on python (import_dicom_study.py) that supports the import of enhanced DICOMs into the tarchive* tables. Feel free to give it a try and migrate towards this new pipeline to ingest DICOMs into LORIS.

LORIS-MRI Release v26.0.3

This is a bug fix release for LORIS-MRI version 26.0 that fixes the following:

• Fix bug when trying to create a session via the DICOM to BIDS python pipeline

List of all LORIS-MRI 26.0.3 changes

Full Changelog: v26.0.2...v26.0.3

LORIS-MRI Release v26.0.2

This is a bug fix release for LORIS-MRI version 26.0 that includes the following fixes for the bids_import.py EEG pipeline:

• [EEG] prePackagedDownloadPath and archive fix by @laemtl in #1213
• Disable chunks with useEEGBrowserVisualizationComponents by @laemtl in #1220

List of all LORIS-MRI 26.0.2 changes

Full Changelog: v26.0.1...v26.0.2

LORIS-MRI Release v26.0.1

This is a bug fix release for LORIS-MRI version 26.0 that includes the following fix for the bids_import.py EEG pipeline:

• Fix various issues with the EEG pipeline #1212
• Introduce a new script tools/delete_physiological_file.py to handle deletion of a EEG file and its metadata on the DB and optionally the filesystem. #1212

List of 26.0.1 changes

Full Changelog: v26.0.0...v26.0.1

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)