From ed022a7393ab6262a11b56b0872d6a4caf484818 Mon Sep 17 00:00:00 2001 From: bids-maintenance Date: Sat, 4 Jul 2020 08:32:01 +0000 Subject: [PATCH] [DOC] Auto-generate changelog entry for PR #513 --- src/CHANGES.md | 167 ++++++++++++++----------------------------------- 1 file changed, 48 insertions(+), 119 deletions(-) diff --git a/src/CHANGES.md b/src/CHANGES.md index 75be7791fe..e59d33840f 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,7 +2,13 @@ ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- \[INFRA] add copyright holder to license. [#521](https://github.com/bids-standard/bids-specification/pull/521) ([sappelhoff](https://github.com/sappelhoff)) +- \[ENH] Update `beh/` specification to contrast with any neural recordings [#515](https://github.com/bids-standard/bids-specification/pull/515) ([effigies](https://github.com/effigies)) - \[Fix] 'segmentation' spelling in 05-derivatives/03-imaging.md [#514](https://github.com/bids-standard/bids-specification/pull/514) ([rwblair](https://github.com/rwblair)) +- \[FIX] restructure and clarify \*\_physio/\*\_stim section [#513](https://github.com/bids-standard/bids-specification/pull/513) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] clarify file formats in EEG, iEEG [#511](https://github.com/bids-standard/bids-specification/pull/511) ([sappelhoff](https://github.com/sappelhoff)) +- \[Fix] Add links and release dates to pre GH changelog, fix formatting [#509](https://github.com/bids-standard/bids-specification/pull/509) ([sappelhoff](https://github.com/sappelhoff)) +- \[INFRA] make circle artifact link a GH action, point to pdf [#505](https://github.com/bids-standard/bids-specification/pull/505) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Typos in DECISION-MAKING file [#504](https://github.com/bids-standard/bids-specification/pull/504) ([tsalo](https://github.com/tsalo)) - \[ENH] Add `Commenting on a PR` to CONTRIBUTING.md [#490](https://github.com/bids-standard/bids-specification/pull/490) ([franklin-feingold](https://github.com/franklin-feingold)) - \[FIX] clarify MEG empty-room recording naming conventions [#480](https://github.com/bids-standard/bids-specification/pull/480) ([sappelhoff](https://github.com/sappelhoff)) @@ -238,164 +244,87 @@ - Adding code of conduct [#6](https://github.com/bids-standard/bids-specification/pull/6) ([chrisgorgo](https://github.com/chrisgorgo)) - Renaming the main document [#1](https://github.com/bids-standard/bids-specification/pull/1) ([chrisgorgo](https://github.com/chrisgorgo)) -## 1.1.1 +## [1.1.1](https://doi.org/10.5281/zenodo.3759805) (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. - +- 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 +## [1.1.0](https://doi.org/10.5281/zenodo.3759802) (2018-04-19) - Added support for MEG data (merged BEP008) -- Added SequenceName field. +- Added `SequenceName` field. - Added support for describing events with Hierarchical Event Descriptors \[[4.3 Task events](04-modality-specific-files/05-task-events.md)]. -- Added VolumeTiming and AcquisitionDuration fields \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. -- Added DwellTime field. +- Added `VolumeTiming` and `AcquisitionDuration` fields \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `DwellTime` field. -## 1.0.2 +## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18) - Added support for high resolution (anatomical) T2star images \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. - - Added support for multiple defacing masks \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. - -- Added optional key and metadata field for contrast enhanced structural scans - \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)] - -- Added DelayTime field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. - +- Added optional key and metadata field for contrast enhanced structural scans \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)] +- Added `DelayTime` field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. - Added support for multi echo BOLD data \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. -## 1.0.1 - -- Added InstitutionName field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. - -- Added InstitutionAddress field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. - -- Added DeviceSerialNumber field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. - -- Added NumberOfVolumesDiscardedByUser and - NumberOfVolumesDiscardedByScanner field \[[4.1 Task (including - resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13) -- Added TotalReadoutTime to functional images metadata list -  \[[4.1 Task (including resting state) imaging - data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `InstitutionName` field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `InstitutionAddress` field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `DeviceSerialNumber` field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added `TotalReadoutTime to` functional images metadata list \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. ## 1.0.1-rc1 -- Added T1 Rho maps \[[4.1 Anatomy imaging - data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. - -- Added support for phenotypic information split into multiple files - \[[3.2 Participant key file](03-modality-agnostic-files.md#participants-file)]. - +- Added T1 Rho maps \[[4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. +- Added support for phenotypic information split into multiple files \[[3.2 Participant key file](03-modality-agnostic-files.md#participants-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. - +- Added `SoftwareVersions` +- Added `run-` 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 `trial_type` column to the event files. +- Added missing `sub-` 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 - -- Added ability to specify fieldmaps acquired with multiple parameter - sets. +## [1.0.0](https://doi.org/10.5281/zenodo.3686062) (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. +- 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” +- 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 -  and - ). - -- 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). - +- 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 and ). +- 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. +- 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-