[Freesurfer] BIDS-PET extension request for comments - closes on Friday, Feb. 12

[Franklin Feingold]

External Email - Use Caution

We are happy to announce that the Positron emission tomography BIDS extension 
is finally nearing it’s completion. Hence, we are seeking final community 
feedback for the PET BIDS standard. We are looking for feedback on GitHub and 
specifically to the BIDS-PET extension proposal ( 
https://secure-web.cisco.com/18Ho2R5GZxtyWMrxs5QijrXyOtATKVsoJi_C5x9ERZG379ee_cw7JF7r45dJV2da4LKI2NNRUy9sGqah-0cOa_Bc6VSabeo33t46e_9DaMfJKU7ABLBpfZi8xyjKlATTBjt3gCWs6LYpvicFDaC2SqlEAh0fst1B0fuFvvxNwmNStQCKL_VuZ5juKj4WMyJ6SQF_m71Ckd4bnPVMjSAKsBqaUku6rb8c7-HjPz3nAxkut6Nk9Cz99XhAwIel-nBHS0CxuBxjGuOt3JAvot58rjA/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fpull%2F633
 ). We have also developed an extension for the validator ( 
https://secure-web.cisco.com/1DgfuUr_8N83-nl-GVdF77jT1sDjVqo-4lsli0XrQ3TOkX5yBoCPoGPYIcPjA_Mnxq_RGrsSoqd_oscs1RZqwh1YuXHb37SJh2GSyfoppehVK2lmz2N5MdwZb-wXjGZoTccWH2Xn2uLEKpUKtzgynUSbIADxpulOf3HsDMOLzioqVA-uHeYbnEODVQyqxun6-m3c6RQM9PWFRTjB5y6mhnqc_rjKmVk8HCHEC3ZbBEyFNMdPK6Mhm5yezOhfhymmekFO0qYOpK1wqgvFedOi81g/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-validator%2Fpull%2F1088
 ) and added PET examples into BIDS examples ( 
https://secure-web.cisco.com/1wcZumOdpBZTibGDOVnAaiUqg8mWF2RuYFeqp6qHGuwgbxUau4PqYYVaD-iLy8iEUT9Ow3hDrJ2uOJwYkjl1iIrKYdwILaW1qwdGo49Ib4fqHhgehv_a7NHZF_rnIrw8P-gJlhBj9OBSUL7fgedLPv-V4K20sjuEIZgtDFf7QA5ykX_6zWs5GoGK9JyiN14TCflmgIdhEyUVrh_Vzt1NAXF49o7DCJNI6CCjgFmc_LaPq98tmEBbPLq8xMY0f5t6_8hNtNAh6xVsLm5TZ_g/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-examples%2Ftree%2Fbep009_pet
 ). The community review will close on Friday (Feb. 12) at 11:59pm PT (pacific 
time).



This BIDS extension seeks to establish how PET data and additional metadata are 
organized within the BIDS structure. This encompasses the recent guidelines for 
brain PET data in publications and in archives provided in the consensus paper 
(Knudsen et al. 2020, 
https://secure-web.cisco.com/1MIWMgeigCAuC-K3Vo4dwvsJCklRfo3-nj_Avatf4FkWMOawTcPrfz1RKd1svX27cs-AjgpYIDrT63jb2G-muHjpKjiTvRq9d8jWYqnymru7rWxU5AnEJzNmanBs13iOBNazfJMm7u0fn_KnB_piCvSUWv9DSw07hQ1VhtnH5lPDgItXKmYx0u8LSm-OdWkWVHpKlfVgfEY4E78qT2J21Y5k2IQIJavfMCucEhWg6ptZjsvh6WR1x-vABTj3nhSI7YMXArof-rba5j3Zuzlj6yQ/https%3A%2F%2Fjournals.sagepub.com%2Fdoi%2F10.1177%2F0271678X20905433
 ), including blood and metabolite data.



The final review entails a two week period for public commenting, with a 
possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (Please see our release protocol for more details,  
https://secure-web.cisco.com/1YsYtZpSMYV6IeNX0JH4epLt99zW9k-K7bPF3XTD3j9llSkw4RQYmhVa8F6dBd-6zh3ZNcWn3d8DZtTXK8cvk_1BZXRDOZBLIh34dNQz20Se-0CgDMDLErCyKt4eoYvmZfexu7PPsD0qkWUE3LVvmzmmCE4o6hR1Y0rZDJHZhAC-dDNLFtPrCHCLfcUNuK3L4YUWDW_y0JExHZe4rD6c2zl7NJBBR9jLNlRF0uCLs7g8fQATsS5Xe9JkWDKODGuRIkqeiqzXH7YeG0yN-9g3nKQ/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fblob%2Fmaster%2FRelease_Protocol.md
 )



We are looking forward to hearing from you,

Melanie Ganz (BEP 009 lead) and team
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[Freesurfer] BIDS-PET extension request for comments - closes on Friday (Jan. 22nd)

[Franklin Feingold]

External Email - Use Caution

We are happy to announce that the Positron emission tomography BIDS extension 
is finally nearing it’s completion. Hence, we are seeking final community 
feedback for the PET BIDS standard. We are looking for feedback on GitHub and 
specifically to the BIDS-PET extension 
proposal.
 We have also developed an extension for the 
validator
 and added PET examples into BIDS 
examples.
 The community review will close on Friday (Jan. 22nd) at 11:59pm PT (pacific 
time).



This BIDS extension seeks to establish how PET data and additional metadata are 
organized within the BIDS structure. This encompasses the recent guidelines for 
brain PET data in publications and in archives provided in the consensus paper 
(Knudsen et al. 
2020),
 including blood and metabolite data.



The final review entails a two week period for public commenting, with a 
possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (Please see our release 
protocol
 for more details)



We are looking forward to hearing from you,

Melanie Ganz (BEP 009 lead) and team
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[Freesurfer] BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed}

[Franklin Feingold]

External Email - Use Caution

The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) 
extension. The updated draft is available for review at: 
https://secure-web.cisco.com/19iI4s--bs7Y_Tdzvgf_eO4rOWt7fabvAARvcNytKJYcOiFI6gGONKUG4ASQvypqsJms2A8I_a2oiLM9epfyjdHtyXW6CaNjs-zFsB_dB6GOFCZjkphCKIXh58QzBtMdlVxRojSk3ksyJJ0amn1AAmltb56n3xoeIneV_uYbxiR-mQaA9pzH2ocGhCflORlUq0kaNtEPAGgtsQXz111gtqA/https%3A%2F%2Fbids-specification--652.org.readthedocs.build%2Fen%2F652%2F04-modality-specific-files%2F01-magnetic-resonance-imaging-data.html%23arterial-spin-labeling-perfusion-data,
 and comments and suggestions may be submitted on GitHub at: 
https://secure-web.cisco.com/1e1-qVFLFl7Vo9V2lZkAqUWA79qa_CZHfymhuxcQvkG9OahetuQhti5mRNs3fI4XCNl00pT4ocbt0U-ovp3zM0uD6zBtJM5aThGTfU8rgXiAaUnAyTObri4Eh_Idgb6oEHWGJpb4-FlBpTvZ4J5zXCQzzFER4BNxuiOodRiiDtQsV0Uqn8Q5HEu6cwue8U8DmfyD04TBeqzZeF3EZfNF8Lw/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fpull%2F652.
 The community review will close on Friday (Nov 13) at 11:59pm PT (pacific time)


This BIDS extension seeks to establish how ASL data and additional metadata are 
organized within the BIDS structure. This encompasses the ASL sequences 
provided in the consensus paper [Alsop 2014], including single- and multi-time 
point pulsed and (pseudo)-continuous ASL.


The final review entails a two week period for public commenting, with a 
possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (For more details on the release protocol, see 
https://secure-web.cisco.com/18WQObGNOBtv6TPfRTvCtrEQv4TE4obqTEzfsuYxPZfeIyFZ1VzLppLkIzVdd0dE5ifMy0KS_NalQuGW_sfnIOBnPrAeVY2JSlAxNyQQlA7B0pUjy-JAq3e1KcT7PR0lhenu1jqSlP6b9DgHpCvLsOGnGq885qi1l_5OyXWoJgab_2b-XgBTpqKFHCS0NYXqYlohILs7SUWyFPbO94Ixp8Q/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fblob%2Fmaster%2FRelease_Protocol.md)


We look forward to hearing your feedback!

The BIDS Team


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[Freesurfer] BIDS-ASL request for comments - closes on Friday (Nov 13th) {Disarmed}

[Franklin Feingold]

External Email - Use Caution

The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) 
extension. The updated draft is available for review at: 
https://secure-web.cisco.com/1t4ZzOsfsvFPLRNF1xylkG0C9rf6FgtaTu4o9Dl7kHsW-tzrZVgK77RfeUpAcEoMP4o6RRVZ4R45vZr_1JxxHGxb4zc1AscgLmhMoMIsa9FTX_r4e37QXoL_APp9N89iIpgamp_RQFcgL1eX_wfl9KZf5ENQZCqsIqH7CvnMJBg4yCaexXyw2xVLkQX6CTglA3_ZZrafG9WTyzTK2b2-gTQ/https%3A%2F%2Fbids-specification--652.org.readthedocs.build%2Fen%2F652%2F04-modality-specific-files%2F01-magnetic-resonance-imaging-data.html%23arterial-spin-labeling-perfusion-data,
 and comments and suggestions may be submitted on GitHub at: 
https://secure-web.cisco.com/1t-cwOKt3nXAzHIaWkuGHBb65JPjrqfPcOYnnZQEzarKcv5VXbbeaBbfIJyLu2DVnJuteaYO42sWVpVy2LpdVCslt36IFJQjhquzIgX_Du0BxBmPPZ2zF-bM3ZRWtF_ri-PUIHicP6_9Vc4HXdBO-iorT4FYqkV3BhT9JnU1daXNfVJfs1wGCiP28h49zTjMP7PoaPKRfSGXLdxUT8K56Ow/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fpull%2F652.
 The community review will close on Friday (Nov 13th) at 11:59pm PT (pacific 
time)


This BIDS extension seeks to establish how ASL data and additional metadata are 
organized within the BIDS structure. This encompasses the ASL sequences 
provided in the consensus paper [Alsop 2014], including single- and multi-time 
point pulsed and (pseudo)-continuous ASL.


The final review entails a two week period for public commenting, with a 
possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (For more details on the release protocol, see 
https://secure-web.cisco.com/1rOmCmEOGynPW9BtbEF5JrCcnOVHiOPW6DHkVog_QFYll7HH7zoIcb2f35VIYicdAPELgjYv3bBwdFgpLS_fJt8kQ166g4k_pidHHn8y0NXXfBobq8b3u4MAKzYL3BeeGanLh41Zp9uu0QNBd3MwnyjA9eZrEyz45x9ym8g-5WrU6Q-fQJtcZFbGiZXPmRwFP0OZOa5n7O5vxqVXtxJXIww/https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fblob%2Fmaster%2FRelease_Protocol.md)


We look forward to hearing your feedback!

The BIDS Team
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[Freesurfer] BIDS Common Derivatives released

[Franklin Feingold]

External Email - Use Caution

Hello!


The BIDS community is proud to announce the release of Common Derivatives! 
Derivatives are the outputs of preprocessing pipelines, capturing data and 
meta-data sufficient for a researcher to understand and (critically) reuse 
those outputs in subsequent pipelines. This specification can be found at: 
https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html


Common principles for derivative datasets:


  *   Derivative datasets describe the contents of the dataset, the methods by 
which it was generated, and the original dataset(s) that were used to generate 
it. This metadata is mandatory at the dataset level and optional at the file 
level.
  *   Derivative files must be distinguishable from raw files. A generic 
description (desc-) entity allows this if no other entity applies.
  *   The spatial interpretation of data, if applicable, can be specified with 
a space entity and SpatialReference metadata.


Releasing the common principles for derivative datasets will enable further 
progress into our modality specific derivative initiatives such as, 
electrophysiological, PET, and 
diffusion MRI. Our immediate 
attention will shift to focus on specifying anatomical and functional 
derivatives (Look out for the pull requests soon!). BEP 028: 
(provenance) is a 
closely related effort that we hope to see progress quickly as well!


We would like to thank our incredible community of contributors and members 
that helped push this extension over the finish line!


Thank you,

Chris and Franklin - BIDS Maintainers
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[Freesurfer] BIDS Derivatives final request for comments

[Franklin Feingold]

External Email - Use Caution

The BIDS community is preparing to merge the Common Derivatives extension. The 
updated draft is available for review at 
https://bids-specification.readthedocs.io/en/common-derivatives/, and comments 
and suggestions may be submitted on GitHub at 
https://github.com/bids-standard/bids-specification/pull/265.


The scope of this extension is establishing a set of common principles for 
organizing derivative datasets, dataset-level metadata, and naming conventions 
for minimally preprocessed files. Additionally, some common imaging derivatives 
(e.g., brain masks) have been specified. More detailed modality-specific 
derivatives are scheduled for inclusion in the next few months.


The final review process entails a minimum of one week for public comment, with 
a possibility of extension for unresolved discussion. Once public comments are 
concluded, there will be a one week freeze, during which only critical issues 
will be considered. (For more details on the release protocol, see 
https://github.com/bids-standard/bids-specification/blob/master/Release_Protocol.md.)


We look forward to hearing your feedback!

Franklin
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[Freesurfer] BIDS v1.3.0 release and next focus

[Franklin Feingold]

External Email - Use Caution

The Brain Imaging Data Structure (BIDS) 
community is pleased to announce version 1.3.0 of the BIDS standard! This 
release includes the addition of genetic 
descriptors
 for linking BIDS datasets to genetic datasets. We would like to thank 
contributors to the Genetic Information BIDS Extension Proposal, led by Cyril 
Pernet, Clara Moreau with contributions from Tom Nichols and Jessica Turner. 
We’d also like to thank Arshitha Basavaraj and Tom Nichols for rendering the 
specification as a PDF.

Our next priority will be finalizing the specification of 
BIDS-Derivatives. 
Please feel free to review the 
draft
 and comment. The specification of spatial references, in particular composite 
surface/volume spaces, remains an open 
question with 
room for expert review.

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[Freesurfer] BIDS 1.2.2 release and Genetic Information feedback

[Franklin Feingold]

External Email - Use Caution

We are excited to announce the release of BIDS version 1.2.2! This release 
enhanced the specification through additional clarifications and smaller fixes. 
The new recently released versions can be found at: 
https://bids-specification.readthedocs.io/en/stable/ along with the complete 
changelog.


In addition, BIDS is calling a final round of comments on the Genetic 
Information extension 
proposal! Please 
review this extension proposal and leave your feedback - we aim to merge this 
extension soon!


Shout out to the Genetic Information BIDS Extension Proposal leads: Cyril 
Pernet, Clara Moreau, Tom Nichols, and Jessica Turner!


Thank you!
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[Freesurfer] BIDS Governance and Steering Group election closing tomorrow!

[Franklin Feingold]

External Email - Use Caution

Time is running out to vote on our BIDS Governance document 
(https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY141o/edit)
 and for the inaugural Steering Group 
(https://docs.google.com/document/d/1yb6j3a90serWbtab7ukSMyecs16sGfYTSGftH-4ArvA/edit)!
 Voting closes tomorrow October 15, 2019, at 11:59pm Pacific Daylight Time (UTC 
-7). Votes will be recorded using a Google form 
(https://forms.gle/YT5SvPgACHhVvf6x8) and a separate form for email validation 
(https://docs.google.com/forms/d/1zr-w3M2K7ApaW3yePXNRc1zYMhIiDsOVnG15nJ1sgx4/edit)
 to make sure the vote is confirmed. We created separate forms to dissociate 
contact information from voting information, and no attempt will be made to 
re-associate these data. Contact information will be used to ensure that the 
number of votes matches the number of voters. All email addresses will be 
deleted immediately once the election results have been verified, with the 
exception of voters who opt to have their email address retained.

If you have any questions regarding this process or BIDS please feel free to 
email Franklin ([ff...@stanford.edu](mailto:ff...@stanford.edu))

Thank you for taking the time to vote!
Franklin


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[Freesurfer] BIDS Governance and Steering Group voting has opened!

[Franklin Feingold]

External Email - Use Caution

The time has come to vote on our BIDS Governance document 
(https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY141o/edit?usp=sharing)
 and for the inaugural Steering Group 
(https://docs.google.com/document/d/1yb6j3a90serWbtab7ukSMyecs16sGfYTSGftH-4ArvA/edit?usp=sharing)!
 Voting opens today (October 1) and runs through October 15, 2019, closing at 
11:59pm Pacific Daylight Time (UTC -7). Votes will be recorded using a Google 
Form 
(https://docs.google.com/forms/d/e/1FAIpQLSfG76N3dnazONsfCsWAXccgrizmb1gm233pJSow3TmTUi3_Fw/viewform)
 and a separate form for email validation 
(https://docs.google.com/forms/d/1zr-w3M2K7ApaW3yePXNRc1zYMhIiDsOVnG15nJ1sgx4/edit)
 to make sure the vote is confirmed. The forms have been created separately to 
dissociate contact information from voting information, and no attempt will be 
made to re-associate these data. Contact information will be used to ensure 
that the number of votes matches the number of voters, making fraudulent voting 
easier to detect. The verification form allows voters to opt-in to having their 
email retained for this purpose. All email addresses will be deleted 
immediately once the election results have been verified, with the exception of 
voters who opt to have their email address retained.



Ratification of the Governance Document is a mandatory vote, with “Yes” 
indicating approval of the document, and “No” indicating rejection. A simple 
majority of “Yes” votes will ratify the document. Failure to achieve a majority 
will nullify the election.



Steering Group candidates are organized into slates of five candidates, and the 
winning slate will form the inaugural Steering Group. Slates are voted on 
according to a ranked ballot, with the preferred slate ranked as “1”, second 
choice as “2”, and so on. Votes will be tabulated according to the 
instant-runoff (https://en.wikipedia.org/wiki/Instant-runoff_voting) method. A 
ballot will be considered invalid if multiple slates receive the same rank.



In addition, we are getting very close to finalizing our BIDS-Derivatives 
extension! We are looking for more feedback from community! The relevant 
conversations can be found in a GitHub pull request 
(https://github.com/bids-standard/bids-specification/pull/265). This pull 
request has identified a few conversations left to reach a consensus before the 
final review!



If you are interested in particular modalities in BIDS, we have established 
teams on GitHub 
(https://github.com/bids-standard/bids-specification/issues/285) to more easily 
follow the conversations that are most relevant to you! We also have a starter 
kit (https://github.com/bids-standard/bids-starter-kit) to help you get started 
using BIDS or finding ways to contribute to the effort!



If you have any questions regarding this process or BIDS please feel free to 
email Franklin (ff...@stanford.edu)



Thank you in advance for taking the time to vote!
Franklin
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[Freesurfer] BIDS Steering Group nominations

[Franklin Feingold]

External Email - Use Caution

Hi FreeSurfer!



We are announcing the nomination period for our fellow colleagues (or 
self-nomination) to the BIDS Steering Group! The BIDS Steering Group is 
proposed within our governance 
document.
 This group is charged with preserving the longevity and sustainability of the 
BIDS standard. This will be a 5 person group that represents different 
modalities and perspectives. To nominate please fill out this 
form. We will be running the nominations 
until August 28 at 11:59pm PST.

Thank you!

Franklin

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