Yaroslav Halchenko issues

Results 840 issues of


                                            Yaroslav Halchenko

Initial question for survey to seek the way to improve adoption

enable preview for PRs?

I guess would need smth like https://github.com/marketplace/actions/deploy-pr-preview . Inspired by inability to see the result in #294

links and resources is ... underwhelming

I was looking for a list of tools and got to https://bids-standard.github.io/bids-starter-kit/links.html which seems to be really "basic". Should point to BIDS-Apps, various other currently existing, possible get rid of...

Add codespell config, workflow and get it to fix some typos it finds

### Description codespell is great, and it can help to keep your code typos free. ### Types of changes - [ ] Bugfix - [ ] New feature - [...

reproin: might want to change logic for dups to actually use datetime not seq number

As discovered in - https://github.com/spatialtopology/spacetop-prep/issues/57#issuecomment-1961651646 we could have "wrong" sequence numbers e.g. upon restart of the scanner.

why release check said it is not needed?

@jwodder any immediate idea why ![image](https://github.com/nipy/heudiconv/assets/39889/71deabf7-cd2d-4239-8eb2-934cd8278a5f) even though we had many PRs merged and recent one then had `release` label?

Add/Extend dataset_description.json:GeneratedBy with information about heudiconv/heuristic (if possible)/dcm2niix

ATM we are recording ad-hoc fields for heudiconv and dcm2niix does the same. Since released in BIDS 1.9.0 - https://github.com/bids-standard/bids-specification/pull/440 there is GeneratedBy which is already used by some datasets....

Implement run+? which would make increment within that sequence

request by @dnkennedy TODOs - [ ] make sure does not break existing - [ ] add tests for +? mode

minor

support dcm2niix "Bidsguess"

Tireless @neurolabusc has developed https://github.com/rordenlab/dcm2niix/tree/development/BidsGuess which would populate `BidsGuess` field in sidecar .json files with `dcm2niix`'s guesses for modality type and entities, e.g. "BidsGuess": ["anat","_acq-tse2_run-3_PDw"], "BidsGuess": ["anat","_acq-tse2_run-3_T2w"], I guess we...

enhancement

ENH: raise exception if dcm2niix returns with non-0 code

apparently we do not fail whenever dcm2niix fails. I think it might have been some change in behavior, may be in nipype? apparently there is odd difference in nipype invocation...