- correct dicom headers
- accept XA30 physio file naming
- merge commits
- dicom_export.py: validate frame counts of all acquisitons from a supplied task type
- bids_utils.py: remove refactored code
- extract session number when underscore in subID
- inherit bids keys in EEG file naming
- update dcm2bids to allow eeg-only sessions
- check if eeg data exported before conversion
- bids_utils.py: eeg bids data assigned to bids experiment directory
- run_mne_eeg2bids function to convert brainvision data to bids standard
- export session level resources, specifically for eeg data
- add part-mag and -phase to BIDS names
- xnat_utils.py: include sequence by name
- xnat_utils.py: allow sequences to be skipped by name
- bids_utils.py: make default task for eeg data todo
- bids_utils.py: update download resources to handle non-absolute bids experiment paths
- changes type of skip / include list to str
- bids_utils.py: refactor request string and add resource name to logging
- xnat_utils.py: deleting unused function
- integrate BIDS conversion of physio data
- installation.md: update docs with feat change type to trigger bump version action
- installation.md: fix tags url
- bids_utils.py: add exist_ok param to makedirs
- xnat2bids.py: add modular function dcm2bids for bids conversion pipeline
- dicom_export: add exist_ok to makedirs to resolve synchronization issue
- add path preprocessing for project and subject data
- check bids_experiment_dir path in github runner
- fetch project and subject data when running with --skip-export
- pyproject.toml: remove xnat-dicom-export, xnat-heudiconv, bids_postprocess, and xnat-dcm2bids from pyproject
- xnat2bids.py: provide correct path for bids experiment directory
- support physio data export
- test_xnat_utils.py: update unit tests to check get_project_subject_session function for multisession data
- check if fmap folder exists before bids_postprocess
- remove redundant resourcesURL specification
- limit filesURL to DICOM format files
- test_bids_utils includes label field
- update bids_postprocess to support single or multiple session selection for IntendedFor mapping, implement overwrite flag, and incorporate into xnat2bids pipeline
- refactor test utility function and documentation
- update bids postprocessing to suppost skipping one or multiple sessions
- update dev docs
- update handling session data
- pre-commit-config.yaml: update flake8 location
- pre-commit.yml: update pre-commit action to v3
- extract session suffix from session label for heudiconv
- bids_utils.py: resolve v1_0_8 release bids post-processing bug
- correct processing and update numpy
- insert intendedfor scans into fieldmap and handle sbref protocol name
- manual update of xnat-tools version for poetry
- populate IntendedFor field map object array, resolve protocol naming for sbref derivative
- remove SBREF derivative string matching, now being handled in heudiconv
- add missing field map derivatives
- update to use new xnat host
- revert failed versions
- fixing publish workflow
- make inputs for postprocess CLI consistent with variable names
- add and abstract string preprojecissing of proj, sub, sess
- remove other heudiconv directories that messup overwrite
- remove other heudiconv directories that messup overwrite
- add blank space before heudiconv's overwrite flag
- add blank space before heudiconv's overwrite flag
- capture duplicate warnings
- overwrite: don't ignore errors, and pass flag to heudiconv
- bring back saving the file after setting DICOM header
- Merge pull request #47 from brown-bnc/feat/add-documentation
- --verbose and --very verbose for postprocess
- change the format of CLI inputs to be consistent to unix style
- put dicom-expoert and run-heudiconv back in separate files
- dicom_export: clomplete options/inputs and run through
- WIP: add dicom_export to xnat2bids_typer
- WIP: start skeleton for typer cli for xnat2bids
- Changes the CLI to use typer, adds MkDocs, pre-commit hooks and Github Actions
- bring back lost build-system from pyproject file
- get xnat2bids and tests back working
- adjust sintax for commands in separate files
- transition posprocessing to typer
- tests: add full path and make sequences strings
- tests: add misssing imports
- fixes to logging, seriesDescList indexing and dicom extension (.IMA)
- WIP working on overwrite behavior
- add identifier to logfiles
- check dicom extension, add formatting
- put back the poetry.lock, didn't know it was needed for the docker build
- add session to the path of IntendedFor nii file
- Add files and functions to insert
IntendedForfield - add --session_suffix as a required input
- coloredlogs respect logging level
- add minimal test to have the ability of making sure things don't break
- add --skilist to arguments
- We are now using SSL!
- enter password only once for xnat2bids
- remove heudiconv extras
- make host optional to use default value
- remove bid_validator, fix empty log, parse only know args
- bidsmap now works properly. Add missing arguments
- names are no longer converted to lower-case
- add color to logging
- ask for password, add logging, add sequence list
- remove selected list
- change dicom tags to match bidsname for protocol and series description
- miscelaneous typo/type errors
- use argument bidsmap json file, take logs out of bids directory
- replace undescores for dashes in session and subject labels
- add xnat_tools to module imports
- user variable for bids_root_dir instead of hardcoded path
- add package prefix to imports
- detect multiple runs
- handle aascout planes and mprage rms
- add xnat2bids code
- bring in xnat2bids code from plugin