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Changelog

Unreleased

  • [INFRA] jQuery 3.4.1 → 3.6.0 #875 (DimitriPapadopoulos)
  • [INFRA] Add "codespell" tool to CI checks to catch typos sooner #873 (DimitriPapadopoulos)
  • [FIX] Make subheadings consistent in 06-longitudinal-and-multi-site-studies.md #870 (guiomar)
  • [DOC] add Anthony as maintainer #868 (Remi-Gau)
  • [ENH] Add "ScanRAS" as an accepted coordinate frame for ieeg #866 (alexrockhill)
  • [INFRA] Add .lgtm.yml file for better usage of LGTM CI tool #865 (DimitriPapadopoulos)
  • [FIX] update physio bids name in longitudinal study page examples #863 (Remi-Gau)
  • [INFRA] Enforce consistent line endings via .gitattributes #861 (DimitriPapadopoulos)
  • [INFRA] dos2unix #859 (DimitriPapadopoulos)
  • [INFRA] LGTM recommendation: Unused local variable #853 (DimitriPapadopoulos)
  • [INFRA] LGTM warning: Variable defined multiple times #851 (DimitriPapadopoulos)
  • [FIX] Typos found by codespell #848 (DimitriPapadopoulos)
  • [INFRA] Add basic documentation on how to use metadata table macros #840 (Remi-Gau)
  • [ENH] make "Institutional department name" available for all datatypes #839 (Remi-Gau)
  • [INFRA] use macro to render examples in a "tree" like fashion #837 (Remi-Gau)
  • [FIX] Add angio suffix to the non-parametric aMRI suffix table #835 (tsalo)
  • [FIX] Remove last hardcoded suffix table #833 (tsalo)
  • [MISC] make explicit that EDF+ (and for EEG: BDF+) are included in iEEG / EEG format requirements #831 (sappelhoff)
  • [ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" #825 (CPernet)
  • [FIX] correct file location of scans.tsv file in example #824 (ghisvail)
  • [FIX] Add missing closing parenthesis in 02-common-principle.md #822 (sebastientourbier)
  • [MISC] update available datatypes in specification #819 (sappelhoff)
  • [FIX] document required column order MEG, EEG, iEEG, PET, and fix typo iEEG #818 (sappelhoff)
  • [MISC] make table headers bold #815 (Remi-Gau)
  • [FIX] What is a composite instance? Change to measurement for non MRI modalities? #813 (rob-luke)
  • [ENH] BEP031 - New entity: sample and samples.tsv file #812 (mariehbourget)
  • [ENH] Add device and acquisition metadata for physio files #806 (Remi-Gau)
  • [MISC] Move section on sessions.tsv file: longitudinal files -> modality agnostic files #805 (Remi-Gau)
  • [ENH] Make explicit that "task" metadata applies to "beh" modality #804 (Remi-Gau)
  • [MISC] Make MRI-centric language more general in Events #801 (sappelhoff)
  • [ENH] clarify that entities MUST be unique #800 (sappelhoff)
  • [MISC] deprecate DCOffsetCorrection field from ieeg.json: Use SoftwareFilters field instead #799 (sappelhoff)
  • [FIX] Deprecate ScanDate (PET) in favor of AcquisitionTime in scans.tsv files #798 (mnoergaard)
  • [MISC] add IETF standard link for json #797 (sappelhoff)
  • [INFRA] In PDF, color every other row in table in light gray fill #794 (sappelhoff)
  • [MISC] add link to guide on how to write a good README #793 (sappelhoff)
  • [SCHEMA] Apply schema rules to entity values #792 (tsalo)
  • [INFRA] fix md ci and update ci badges #791 (sappelhoff)
  • [SCHEMA] Use macro for filename templates in file collections appendix #787 (tsalo)
  • [FIX] consistently refer to DICOM Tags throughout the specification #786 (Hboni)
  • [FIX] Amend note about *b*-vecs on DWI specs #782 (oesteban)
  • [INFRA] add CI to find trailing whitespace #780 (sappelhoff)
  • [MISC] Add info on HED key to common principles #777 (sappelhoff)
  • [ENH] add EEGLAB as valid coordinate system for EEG #775 (sappelhoff)
  • [SCHEMA] Add metadata term files #774 (tsalo)
  • [SCHEMA] Add suffix term files #772 (tsalo)
  • [ENH] Allow encoding the fieldmapping intent of the protocol #622 (oesteban)
  • [FIX] Correct iEEG example that contained double suffixes #463 (yarikoptic)

v1.6.0 (2021-04-22)

  • [FIX] Typos discovered by codespell #784 (yarikoptic)
  • REL: v1.6.0 #776 (effigies)
  • [FIX] Rename "Unit" metadata to "Units" for consistency with existing fields #773 (effigies)
  • [FIX] typo in pet: institution -> institutional #771 (sappelhoff)
  • [INFRA] install git in linkchecker job #767 (sappelhoff)
  • [INFRA] Fix CircleCI workflows #764 (sappelhoff)
  • [INFRA] do not run remark on auto CHANGES #755 (sappelhoff)
  • [FIX] Mix up (typo) between ficiduals and landmarks in EEG spec #754 (rob-luke)
  • [INFRA] updating remark, CIs, contributor docs #745 (sappelhoff)
  • [FIX] schema for i/eeg coordsys+elecs: sub-ses-acq-space are allowed entities #743 (sappelhoff)
  • [DOC] move schema documentation into the schema folder #740 (Remi-Gau)
  • [MISC] standardize string examples format in tables #739 (Remi-Gau)
  • [MISC] Clarify participant_id in participants.tsv file if it exists #738 (adam2392)
  • [FIX] split MEG files should be listed separately in scans.tsv #735 (eort)
  • [FIX] 1) Clarify appropriate labels for space entity, 2) Clarify channels+electrodes do not have to match #734 (sappelhoff)
  • [MISC] refactor stimuli mentioning sections in the events page #697 (Remi-Gau)
  • [ENH] Bep 009: Positron Emission Tomography #633 (melanieganz)

v1.5.0 (2021-02-23)

  • [MISC] Updated TotalAcquiredVolumes into TotalAcquiredPairs #742 (effigies)
  • REL: v1.5.0 #736 (franklin-feingold)
  • [SCHEMA] Update qMRI fieldmap schema #728 (effigies)
  • [FIX] Add deprecated anatomical MRI suffixes back into schema #725 (tsalo)
  • [FIX] Correct schema irregularities for func datatype #724 (tsalo)
  • [FIX] Make flip optional for MP2RAGE #722 (tsalo)
  • [FIX] Correct entity names in YAML files #720 (tsalo)
  • [ENH] Clarify run indexing information for MRI acquisitions #719 (effigies)
  • [ENH] Harmonize CoordinateSystem details for MRI, MEG, EEG, iEEG #717 (sappelhoff)
  • [SCHEMA] Update entity YAML keys #714 (effigies)
  • [MISC] Added full names for some contributors in .mailmap file #705 (yarikoptic)
  • [INFRA] Migrate md and yml checks from travis to GH actions #693 (sappelhoff)
  • [INFRA] Move part entity to before recording entity #692 (tsalo)
  • [ENH] BEP001 - qMRI maps and some additional metadata #690 (agahkarakuzu)
  • [ENH] BEP001 - Entity-linked file collections #688 (effigies)
  • [ENH] BEP001 - New entities: inv & mt #681 (agahkarakuzu)
  • [DOC] add contributing guidelines to add figures in the specs #679 (Remi-Gau)
  • [MISC] use RFC 2119 language in legend of the "volume timing" table #678 (Remi-Gau)
  • [FIX] Add OPTIONAL acq entity to channels.tsv, events.tsv to match electrophysiological acquisitions #677 (sappelhoff)
  • [MISC] Update all links to use HTTPS whenever possible. #676 (gllmflndn)
  • [INFRA] Relax line length limit for linting YAML files #673 (effigies)
  • [ENH] BEP001 - New entity: flip #672 (agahkarakuzu)
  • [ENH] BEP001 - RepetitionTimeExcitation and RepetitionTimePreparation #671 (agahkarakuzu)
  • [ENH] Bep 005: Arterial Spin Labeling #669 (sappelhoff)
  • [FIX] Added white space after table #660 (robertoostenveld)
  • [MISC] add remi as maintainer #657 (Remi-Gau)
  • [MISC] update Contributing with info on how to respond to reviews #655 (Remi-Gau)
  • [FIX] add paragraph on MEG specific "markers" suffix in MEG spec #653 (sappelhoff)
  • [FIX] Rewrite the MRI/fieldmaps subsection for consistency with the rest of specs #651 (oesteban)
  • [FIX] Fixing template string on electrodes for eeg and ieeg. #650 (adam2392)
  • [ENH] Update genetics-BIDS citation #646 (effigies)
  • [SCHEMA] Add derivatives entities to the schema #645 (tsalo)
  • [MISC] add brief note that TSV example in the spec may currently use either tab or space characters #643 (yarikoptic)
  • [ENH] Add "multipart DWI" acquisitions and refactor DWI specifications #624 (oesteban)
  • [SCHEMA] Render schema elements in text #610 (tsalo)
  • [ENH] Add part entity for complex-valued data #424 (tsalo)

v1.4.1 (2020-10-13)

  • [INFRA] minor robustness enhancements to pdf build shell script #642 (yarikoptic)
  • [FIX] consistent CoordinateSystem fields for ephys #641 (sappelhoff)
  • REL: v1.4.1 #640 (franklin-feingold)
  • [INFRA] set up github action to detect latin phrases #636 (Remi-Gau)
  • [ENH] Add a definition for "deprecation" #634 (sappelhoff)
  • [MISC] consolidate BIDS citations in introduction #630 (sappelhoff)
  • [FIX] URI "definition" and recommendation #629 (Remi-Gau)
  • [FIX] change remaining latin expressions (etc and i.e.) #628 (Remi-Gau)
  • [FIX] replace "e.g.," by "for example" #626 (Remi-Gau)
  • [FIX] arrays of 3D coordinates MUST supply numeric values in x, y, z order #623 (sappelhoff)
  • [FIX] Accidentally swapped Neuromag/Elekta/MEGIN cross-talk & fine-calibration filename extensions #621 (hoechenberger)
  • [FIX] improve HED documentation #619 (VisLab)
  • [INFRA] Move MRI section headings up a level #618 (tsalo)
  • [INFRA] SCHEMA: Declare entities by concept names, add entity field for filename components #616 (effigies)
  • [FIX] Change wrong text references from *CoordinateSystemUnits to *CoordinateUnits #614 (sappelhoff)
  • [ENH] Describe arbitrary units in Common Principles #606 (tsalo)
  • [FIX] Clarify data types and requirement levels for all JSON files #605 (sappelhoff)
  • [INFRA] downgrade github-changelog-generator to 1.14.3 due to issue with 1.15.2 #600 (sappelhoff)
  • [FIX] tighter rules for sharing MEG cross-talk and fine-calibration .fif files #598 (sappelhoff)
  • [MISC] Add tsalo as a BIDS maintainer #597 (tsalo)
  • [FIX] clarify definition of events in common principles #595 (sappelhoff)
  • [INFRA] use --release-branch option in github-changelog-generator #594 (sappelhoff)
  • [ENH] Define "modality" and clarify "data type" #592 (effigies)
  • [FIX] Adjust index definition to be nonnegative integer #590 (nicholst)
  • [MISC] fix links, make json object links consistent, fix pandoc rendering #587 (sappelhoff)
  • [FIX] Fix link in Common principles #583 (tsalo)
  • [ENH] Specify how to share cross-talk and fine-calibration for Neuromag/Elekta/MEGIN data #581 (sappelhoff)
  • [ENH] Specify echo and run indices are nonnegative integers in schema #578 (tsalo)
  • [ENH] add optional presentation software name, version, OS, and code to events.json #573 (Remi-Gau)
  • [ENH] added PPG as an accepted channel type for EEG, MEG and iEEG #570 (robertoostenveld)
  • [INFRA] Move entity definitions to a separate page #568 (tsalo)
  • [INFRA] enable pandoc emojis for the pdf build #562 (sappelhoff)
  • [INFRA] Auto adjust table fences before PDF conversion #560 (sebastientourbier)
  • [ENH] Support run and acq entities in behavior-only data #556 (tsalo)
  • [FIX] Clarify requirement levels for TSV metadata fields #555 (sappelhoff)
  • [FIX] Reorganize rec, ce entities, _defacemask #550 (emdupre)
  • [FIX] Clarify Upper-casing of Channels.tsv Channel Type #548 (adam2392)
  • [ENH] Extend date time information to include optional UTC syntax, warn about FIF requirements #546 (sappelhoff)
  • [FIX] clarify that <physio|stim>.json is REQUIRED #542 (sappelhoff)
  • [FIX] Replace all non-breaking spaces with vanilla spaces #536 (nicholst)
  • [FIX] Clarify indices are nonnegative integers. #535 (nicholst)
  • [FIX] Clarify use of session entity in file names #532 (Moo-Marc)
  • [ENH] Add the ability of users to specify an explicit HED.xml schema for validation. #527 (VisLab)
  • [FIX] clarify that scans.json is allowed and recommended #523 (sappelhoff)
  • [INFRA] add copyright holder to license. #521 (sappelhoff)
  • [FIX] clarify XXXCoord* in the coordinate systems appendix #520 (sappelhoff)
  • [ENH] Update beh/ specification to contrast with any neural recordings #515 (effigies)
  • [Fix] 'segmentation' spelling in 05-derivatives/03-imaging.md #514 (rwblair)
  • [FIX] restructure and clarify *_physio/*_stim section #513 (sappelhoff)
  • [FIX] clarify file formats in EEG, iEEG #511 (sappelhoff)
  • [Fix] Add links and release dates to pre GH changelog, fix formatting #509 (sappelhoff)
  • [FIX] Clarify that acq\_time in scans.json refers to first data point acquired #506 (tsalo)
  • [INFRA] make circle artifact link a GH action, point to pdf #505 (sappelhoff)
  • [FIX] Typos in DECISION-MAKING file #504 (tsalo)
  • [ENH] Add Commenting on a PR to CONTRIBUTING.md #490 (franklin-feingold)
  • [FIX] clarify MEG empty-room recording naming conventions #480 (sappelhoff)
  • [INFRA] Convert entity table to yaml #475 (tsalo)
  • [FIX] Recommend SI units formatting to adhere to CMIXF-12 #411 (sappelhoff)

v1.4.0 (2020-06-11)

v1.3.0 (2020-04-14)

v1.2.2 (2020-02-12)

v1.2.1 (2019-08-14)

v1.2.0 (2019-03-04)

v1.1.2 (2019-01-10)

1.1.1 (2018-06-06)

  • Improved the MEG landmark coordinates description.
  • Replaced ManufacturersCapModelName in meg.json with CapManufacturer and CapManufacturersModelName.
  • Remove EEGSamplingFrequency and ManufacturersAmplifierModelName from the meg.json.
  • Improved the behavioral data description.

1.1.0 (2018-04-19)

1.0.2 (2017-07-18)

1.0.1 (2017-03-13)

1.0.1-rc1

  • Added T1 Rho maps [4.1 Anatomy imaging data].
  • Added support for phenotypic information split into multiple files [3.2 Participant key file].
  • Added recommendations for multi site datasets
  • Added SoftwareVersions
  • Added run-<run_index> to the phase encoding maps. Improved the description.
  • Added InversionTime metadata key.
  • Clarification on the source vs raw language.
  • Added trial_type column to the event files.
  • Added missing sub-<participant_label> in behavioral data file names
  • Added ability to store stimuli files.
  • Clarified the language describing allowed subject labels.
  • Added quantitative proton density maps.

1.0.0 (2016-06-23)

  • Added ability to specify fieldmaps acquired with multiple parameter sets.
  • Added ability to have multiple runs of the same fieldmap.
  • Added FLASH anatomical images.

1.0.0-rc4

  • Replaced links to neurolex with explicit DICOM Tags.
  • Added sourcedata.
  • Added data dictionaries.
  • Be more explicit about contents of JSON files for structural (anatomical) scans.

1.0.0-rc3

  • Renamed PhaseEncodingDirection values from "x", "y", "z" to "i", "j", "k" to avoid confusion with FSL parameters
  • Renamed SliceEncodingDirection values from "x", "y", "z" to "i", "j", "k"

1.0.0-rc2

  • Removed the requirement that TSV files cannot include more than two consecutive spaces.
  • Refactor of the definitions sections (copied from the manuscript)
  • Make support for uncompressed .nii files more explicit.
  • Added BIDSVersion to dataset.json
  • Remove the statement that SliceEncodingDirection is necessary for slice time correction
  • Change dicom converter recommendation from dcmstack to dcm2nii and dicm2nii following interactions with the community (see moloney/dcmstack#39 and https://github.com/neurolabusc/dcm2niix/issues/4).
  • Added section on behavioral experiments with no accompanying MRI acquisition
  • Add _magnitude.nii[.gz] image for GE type fieldmaps.
  • Replaced EchoTimeDifference with EchoTime1 and EchoTime2 (SPM toolbox requires this input).
  • Added support for single band reference image for DWI.
  • Added DatasetDOI field in the dataset description.
  • Added description of more metadata fields relevant to DWI fieldmap correction.
  • PhaseEncodingDirection is now expressed in "x", "y" etc. instead of "PA" "RL" for DWI scans (so it's the same as BOLD scans)
  • Added rec-<label> flag to BOLD files to distinguish between different reconstruction algorithms (analogous to anatomical scans).
  • Added recommendation to use _physio suffix for continuous recordings of motion parameters obtained by the scanner side reconstruction algorithms.

1.0.0-rc1

  • Initial release

* This Change Log was automatically generated by github_changelog_generator