1.8.1 - 2024-09-19

Changes since 1.8.0

Changed:

• bidsmap_template: Updated to BIDS 1.10.0 and added several new protocols
• BIDSschema validation: BIDS-defined fields that are not defined for current data-type now raises an error
• BIDSschema validation: Extra non BIDS fields now show a warning

Fixed:

• mapper: Error when testing an empty IntendedFor field
• mapper: When retrieving run from template, attributes wasn't adapted to the tested file
• MRI: perf data type wasn't in valid data types

1.8.0 2024-09-12

Changes since 1.7.1

Added

• MRS: support for Magnetic Resonance Spectroscopy

Fixed

• bidsmap: Empty modules no longer saved to bidsmap
• bidsmap: In case of BIDS version change, warning shows incorrect version
• hmriNIFTI: Fixed error of corrupted file on Siemens derivated MRI images lacking CSASeriesHeaderInfo sections

Changed

• bidsmap/run: If modality or suffix not defined, default model will be __unknown__, otherwise <modality>:suffix
• bidsmap/bidsmap: For __unknown__ and __ignore__ modalities, the model will be fixed to __unknown__
• mapper: If suffix is not defined, an error will be shown, and no further vqalidations will be performed on that file
• BidsTable: Updated lineterminator parameter, making it compatible with modern (>1.4) Pandas, and Pythons up to 3.12
• Modules: Base module class selector has been moved into tools, new modalities are no longer decalred in `selector.py

1.7.0 - 2024-06-12

Changes since 1.6.6

Added:

• The sidecar and entities are retrieved from official BIDS schema via bidsschematools
• During mapping, the same schema is used to validate the entities and sidecars
• unittests for schema retrieval and validation
• plugin.tools.General: Functions for helping prepared data curation, namely LoadCurationList, CleanupPrepared and CheckPrepared
• unittests for data curation

Changed

• mapping,bidsification: the list of entities and sidecar fields are extracted from current BIDS schema
  (based on bidsschematools package)
• Python>=3.8, Python<3.11: Restricted python to >=3.8 to satisfy dependence to bidsschematools
• bidsmap: model parameter is now explicitly saved in bidsmap
• bidsmap: model now takes form of <data type>:<suffix> and used to retrieve entities and sidecat fields
• mapping: template == true will now also expand json and entities sections
• Modules: the metadata fields in modality class definitions are now replaced by shotrcuts, which
  links sidecar JSON field with corresponding dynamic field in metadata
• bidsmap: required sidecar json fields that BIDSME can retrieve automatically (in custom variables,
  via shortcuts, or directly in metadata) are now explicetly saved in bidsmap
• unknown map is now created in same folder as bidsmap
• DWI: warning about missing bval/vec files now triggers only for suffix dwi

1.6.6 - 2024-04-25

Changes since 1.5.0

Added

• Modules/base: The series Id and No can now be changed in plugins via attributes recording.series_id and recording.series_no
• MRI/jsonNIFTY: All bids metafields are by default completed from the provided json
• Modules/base: If BIDS metadata has the same name as a custom metadata, then the content of custom metadata is used
• plugins/tools: A tool that uses dcm2niix to convert and merge dicoms after preparation
• Plugin/Nibabel: Convert3Dto4D will also remove json files, not only nifti
• Plugin/Nibabel: Convert3Dto4D will conserve the written data scale, if all merged files have the same slope and intercept
• Log entry while loading tables
• NIFTI: added support for compressed files

Changed:

• Limited support for Python <3.11
• Modules/MRI/Nifti, Modules/PET/Nifti: the header dump is now created by default
• MRI/DICOM: Using nibabel and mri_parser to parse Siemens-specific headers CSAHeaderInfo and CSASeriesInfo
• Plugin/Nibabel: Convert3Dto4D will produce an error when trying merging of 2-file nifti (hdr/img)

Fixed

• bidsify: Error when trying bidsify non-BIDS modalities (issue #29)
• logging output redirected to stdout, and forcing colors (fixing red background in jupyther-lab)
• Import issue for MRI/DICOM when installed pydicom will raise error with not installed dicom-parcer
• Modules/MRI/Nifti, Modules/PET/Nifti: diminfo from header are now retrieved as integer instead of bytes
• Modules/MRI/Nifti, Modules/PET/Nifti: header dump exported as dict, instead of string
• Modules/MRI/bidsmeNifty: Removed error if file was created not from DICOM
• Modules/PET/bidsmeNifty: Removed error if file was created not from DICOM
• Plugins import is explicetely reset in the beginning of preparation/mapping/processing/bidsification
• Plugin/Nibabel: crash in Convert3Dto4D when removing merged files
• jsonNIFTI: fixed retrieval of ParticipantID, based on dcm2niix entry PatientID
• BaseModule: series_no/series_id becomes prperties with type check (int/str resp.)

1.6.5

Changes since 1.5.1

Added

• Modules/base: The series Id and No can now be changed in plugins via attributes recording.series_id and recording.series_no
• MRI/jsonNIFTY: All bids metafields are by default completed from the provided json
• Modules/base: If BIDS metadata has the same name as a custom metadata, then the content of custom metadata is used
• plugins/tools: A tool that uses dcm2niix to convert and merge dicoms after preparation
• Plugin/Nibabel: Convert3Dto4D will also remove json files, not only nifti
• Plugin/Nibabel: Convert3Dto4D will conserve the written data scale, if all merged files have the same slope and intercept
• Log entry while loading tables
• NIFTI: added support for compressed files

Changed:

• Limited support for Python <3.11
• Modules/MRI/Nifti, Modules/PET/Nifti: the header dump is now created by default
• MRI/DICOM: Using nibabel and mri_parser to parse Siemens-specific headers CSAHeaderInfo and CSASeriesInfo
• Plugin/Nibabel: Convert3Dto4D will produce an error when trying merging of 2-file nifti (hdr/img)

Fixed

• logging output redirected to stdout, and forcing colors (fixing red background in jupyther-lab)
• Import issue for MRI/DICOM when installed pydicom will raise error with not installed dicom-parcer
• Modules/MRI/Nifti, Modules/PET/Nifti: diminfo from header are now retrieved as integer instead of bytes
• Modules/MRI/Nifti, Modules/PET/Nifti: header dump exported as dict, instead of string
• Modules/MRI/bidsmeNifty: Removed error if file was created not from DICOM
• Modules/PET/bidsmeNifty: Removed error if file was created not from DICOM
• Plugins import is explicetely reset in the beginning of preparation/mapping/processing/bidsification
• Plugin/Nibabel: crash in Convert3Dto4D when removing merged files
• jsonNIFTI: fixed retrieval of ParticipantID, based on dcm2niix entry PatientID
• BaseModule: series_no/series_id becomes prperties with type check (int/str resp.)

Full Changelog: 1.5.1...1.6.5

1.6.4 - 2024-04-11

Changes since 1.5.0

Added

• Modules/base: The series Id and No can now be changed in plugins via attributes recording.series_id and recording.series_no
• MRI/jsonNIFTY: All bids metafields are by default completed from the provided json
• Modules/base: If BIDS metadata has the same name as a custom metadata, then the content of custom metadata is used
• plugins/tools: A tool that uses dcm2niix to convert and merge dicoms after preparation
• Plugin/Nibabel: Convert3Dto4D will also remove json files, not only nifti
• Plugin/Nibabel: Convert3Dto4D will conserve the written data scale, if all merged files have the same slope and intercept

Changed:

• Limited support for Python <3.11
• Modules/MRI/Nifti, Modules/PET/Nifti: the header dump is now created by default
• MRI/DICOM: Using nibabel and mri_parser to parse Siemens-specific headers CSAHeaderInfo and CSASeriesInfo
• Plugin/Nibabel: Convert3Dto4D will produce an error when trying merging of 2-file nifti (hdr/img)

Fixed

• logging output redirected to stdout, and forcing colors (fixing red background in jupyther-lab)
• Import issue for MRI/DICOM when installed pydicom will raise error with not installed dicom-parcer
• Modules/MRI/Nifti, Modules/PET/Nifti: diminfo from header are now retrieved as integer instead of bytes
• Modules/MRI/Nifti, Modules/PET/Nifti: header dump exported as dict, instead of string
• Modules/MRI/bidsmeNifty: Removed error if file was created not from DICOM
• Modules/PET/bidsmeNifty: Removed error if file was created not from DICOM
• Plugins import is explicetely reset in the beginning of preparation/mapping/processing/bidsification
• Plugin/Nibabel: crash in Convert3Dto4D when removing merged files

1.6.3 - 2024-03-06

Added

• Modules/base: The series Id and No can now be changed in plugins via attributes recording.series_id and recording.series_no
• MRI/jsonNIFTY: All bids metafields are by default completed from the provided json
• Modules/base: If BIDS metadata has the same name as a custom metadata, then the content of custom metadata is used
• plugins/tools: A tool that uses dcm2niix to convert and merge dicoms after preparation
• Plugin/Nibabel: Convert3Dto4D will also remove json files, not only nifti
• Plugin/Nibabel: Convert3Dto4D will conserve the written data scale, if all merged files have the same slope and intercept

Changed:

• Modules/MRI/Nifti, Modules/PET/Nifti: the header dump is now created by default
• MRI/DICOM: Using nibabel and mri_parser to parse Siemens-specific headers CSAHeaderInfo and CSASeriesInfo
• Plugin/Nibabel: Convert3Dto4D will produce an error when trying merging of 2-file nifti (hdr/img)

Fixed

• Modules/MRI/Nifti, Modules/PET/Nifti: diminfo from header are now retrieved as integer instead of bytes
• Modules/MRI/Nifti, Modules/PET/Nifti: header dump exported as dict, instead of string
• Modules/MRI/bidsmeNifty: Removed error if file was created not from DICOM
• Modules/PET/bidsmeNifty: Removed error if file was created not from DICOM
• Plugins import is explicetely reset in the beginning of preparation/mapping/processing/bidsification
• Plugin/Nibabel: crash in Convert3Dto4D when removing merged files

1.5.0

Release for the publication in JOSS

Fixed

• Module/base: Bug when recIdentity() wasn't called as function

Changed

• Several improvements in documentation and README
• Updated links to the examples and tutorial to point to GitHub

1.4.3

Fixed:

• Bug in bidsification when working with bare nifty file
• PET: Updated entities list, remobved some nore more required json metadata
• PET/ECAT: Degraded warning of non-decodable bytes string to debug
• plugins/template: Fixed (finally) the import of classes in template
• MRI/jsonNIFTY, PET/jsonNIFTY: fixed crash when trying to load generic json NIFTY file
• MRI/hmriNIFTY: removed requirement of presence of MrPhoenixProtocol
• plugins: added __init__.py to tools so plugin tools will be properly installed
• bidsMeta: Fixed not reseted bidsSession list of subjects.tsv columns
• plugins.tools: Fixed faulty import of baseModule

Added:

• Integrartion test for GitHub

Changed:

• Table sidecars (including participants.json) now supports extra phields, not related to columns names
• bidsmap: Accepting non-bids modality with a warning
• bidsmap: Runs loaded from template are now unchecked
• README.md: liknks points to GitHub repo
• Splitted bloated README
• Version naming schema for post-release fixes

Removed

• baseModule: removed spanning messages about testing files in scan folders

1.4.2

[1.4.2] - 2023-08-08

Added:

• Integrartion test for GitHub

Fixed:

• PET: Updated entities list, remobved some nore more required json metadata
• PET/ECAT: Degraded warning of non-decodable bytes string to debug
• plugins/template: Fixed (finally) the import of classes in template
• MRI/jsonNIFTY, PET/jsonNIFTY: fixed crash when trying to load generic json NIFTY file
• MRI/hmriNIFTY: removed requirement of presence of MrPhoenixProtocol
• plugins: added __init__.py to tools so plugin tools will be properly installed
• bidsMeta: Fixed not reseted bidsSession list of subjects.tsv columns
• plugins.tools: Fixed faulty import of baseModule

Changed:

• Table sidecars (including participants.json) now supports extra phields, not related to columns names
• bidsmap: Accepting non-bids modality with a warning
• bidsmap: Runs loaded from template are now unchecked
• README.md: liknks points to GitHub repo
• Splitted bloated README
• Version naming schema for post-release fixes

Removed

• baseModule: removed spanning messages about testing files in scan folders