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[MISC] Added appendix to mkdocs and added some internal links #77

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999b897
pull of common elements from starter kit + some edits
patrick-g-h Oct 11, 2018
6c8c073
Update CONTRIBUTING.md
patrick-g-h Oct 12, 2018
3bdca0c
Update CONTRIBUTING.md
patrick-g-h Oct 12, 2018
1f6f59e
Merge pull request #3 from bids-standard/master
franklin-feingold Oct 12, 2018
0a5654f
Update CONTRIBUTING.md
franklin-feingold Oct 12, 2018
36b8caa
Merge branch 'patch-1' into master
patrick-g-h Oct 22, 2018
d99e4fa
Merge pull request #4 from bids-standard/master
franklin-feingold Oct 24, 2018
63c245a
Add files via upload
franklin-feingold Oct 24, 2018
184b868
Small edit
franklin-feingold Oct 24, 2018
98cd127
Small edit
franklin-feingold Oct 24, 2018
6a6c963
Merge pull request #5 from bids-standard/master
franklin-feingold Oct 30, 2018
c3a6530
Edits and Additions of Appendix into mkdocs
franklin-feingold Oct 30, 2018
68028d5
Delete 02-common-principles.md
franklin-feingold Oct 30, 2018
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Delete 02-magnetoencephalography.md
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franklin-feingold Oct 30, 2018
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Delete 03-task-events.md
franklin-feingold Oct 30, 2018
8965b8b
update 02 common and 03 modality agnostic
franklin-feingold Oct 30, 2018
f4a3821
update 02 MEG and 03 task
franklin-feingold Oct 30, 2018
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old contributing
franklin-feingold Oct 30, 2018
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Changes links updated
franklin-feingold Oct 30, 2018
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update 02,03
franklin-feingold Oct 30, 2018
e5daf84
update 04/02,03
franklin-feingold Oct 30, 2018
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Update 02-magnetoencephalography.md
franklin-feingold Oct 30, 2018
b29ae39
corrected 02-meg links
franklin-feingold Oct 30, 2018
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small edit
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make remark happy
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110 changes: 78 additions & 32 deletions CHANGES.md
Original file line number Diff line number Diff line change
@@ -1,118 +1,164 @@
1 Changelog <a id="h.17phlwhk50et"></a>
===============
1 Changelog

1.1.1

- Improved the MEG landmark coordinates description.
- Replaced ManufacturersCapModelName in meg.json with CapManufacturer
and CapManufacturersModelName.

- Replaced ManufacturersCapModelName in meg.json with CapManufacturer and
CapManufacturersModelName.

- Remove EEGSamplingFrequency and ManufacturersAmplifierModelName
from the meg.json.
from the meg.json.

- Improved the behavioural data description.

1.1.0

- Added support for MEG data (merged BEP008)
- Added SequenceName field.
- Added support for describing events with Hierarchical Event Descriptors [[8.5 Task events](#heading=h.daip42kp5ndz)].
- Added VolumeTiming and AcquisitionDuration fields [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added DwellTime field.
- Added support for MEG data (merged BEP008)
- Added SequenceName field.
- Added support for describing events with Hierarchical Event Descriptors [[4.3 Task events](src/04-modality-specific-files/03-task-events.md)].
- Added VolumeTiming and AcquisitionDuration fields [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
- Added DwellTime field.

1.0.2

- Added support for high resolution (anatomical) T2star images [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
- Added support for multiple defacing masks [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
- Added optional key and metadata field for contrast enhanced structural scans [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)].
- Added DelayTime field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added support for multi echo BOLD data [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added support for high resolution (anatomical) T2star images [[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].

- Added support for multiple defacing masks [[4.1 Anatomy imaging data](src/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](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]

- Added DelayTime field [[4.1 Task (including resting state) imaging data](src/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](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].

1.0.1

- Added InstitutionName field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added InstitutionAddress field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added DeviceSerialNumber field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)].
- Added InstitutionName field [[4.1 Task (including resting state) imaging data](src/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](src/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](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].

- Added NumberOfVolumesDiscardedByUser and
NumberOfVolumesDiscardedByScanner field [[8.4 Task (including
resting state) imaging data](#heading=h.r8mrcau3kkcq)].
NumberOfVolumesDiscardedByScanner field [[4.1 Task (including
resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].

- Added TotalReadoutTime to functional images metadata list
 [[8.4 Task (including resting state) imaging
data](#heading=h.r8mrcau3kkcq)].
 [[4.1 Task (including resting state) imaging
data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].

1.0.1-rc1

- Added T1 Rho maps [[8.3 Anatomy imaging
data](#heading=h.fm6ipijipc08)].
- Added T1 Rho maps [[4.1 Anatomy imaging
data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)].

- Added support for phenotypic information split into multiple files
[[8.11 Participant key file](#heading=h.pi5iigxxt8vy)].
[[3.2 Participant key file](src/03-modality-agnostic-files.md#participants-file)].

- Added recommendations for multi site datasets

- Added SoftwareVersions

- Added run-&lt;run_index&gt; 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-&lt;participant_label&gt; in
behavioural 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.

- 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
[https://github.com/moloney/dcmstack/issues/39](https://github.com/moloney/dcmstack/issues/39) and
[https://github.com/neurolabusc/dcm2niix/issues/4](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)

- 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-&lt;label&gt; 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.
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
- Initial release
9 changes: 9 additions & 0 deletions mkdocs.yml
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Expand Up @@ -16,4 +16,13 @@ nav:
- Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md
- Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioural-experiments.md
- Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md
- Appendix:
- Contributors: 99-appendices/01-contributors.md
- Licenses: 99-appendices/02-licenses.md
- HED: 99-appendices/03-hed.md
- Entity-table: 99-appendices/04-entity-table.md
- Units: 99-appendices/05-units.md
- MEG file formats: 99-appendices/06-meg-file-formats.md
- MEG systems: 99-appendices/07-meg-systems.md
- Coordinate-systems: 99-appendices/08-coordinate-systems.md
- The BIDS Starter Kit: https://github.com/bids-standard/bids-starter-kit
2 changes: 1 addition & 1 deletion src/02-common-principles.md
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Expand Up @@ -298,7 +298,7 @@ SI derived units. In case there are valid reasons to deviate from SI units or SI
derived units, the units MUST be specified in the sidecar JSON file. In case
data is expressed in SI units or SI derived units, the units MAY be specified in
the sidecar JSON file. In case prefixes are added to SI or non-SI units (e.g.
mm), the prefixed units MUST be specified in the JSON file (see Appendix V:
mm), the prefixed units MUST be specified in the JSON file (see [Appendix V](99-appendices/05-units.md):
Units). In particular:

- Elapsed time SHOULD be expressed in seconds. Please note that some DICOM
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3 changes: 2 additions & 1 deletion src/03-modality-agnostic-files.md
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Expand Up @@ -104,7 +104,8 @@ kept in phenotype/ folder and end with the `.tsv` extension. They can include
arbitrary set of columns, but one of them has to be participant_id with matching
`sub-<participant_label>`. As with all other tabular data, those additional
phenotypic information files can be accompanied by a JSON file describing the
columns in detail (see Section 4.2). In addition to the column description, a
columns in detail (see [here](02-common-principles.md#tabular-files)).
In addition to the column description, a
section describing the measurement tool (as a whole) can be added under the name
`MeasurementToolMetadata`. This section consists of two keys: `Description` - a
free text description of the tool, and `TermURL` a link to an entity in an
Expand Down
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