Yaroslav Halchenko

is .zarr/ suffix strictly required? any other ".subsuffixes." considered (like in .ome.zarr)

3

For DANDI we are considering to implement custom support for zarr "filesets" versioning. There is an experimental webdav which is reverse proxied by apache at is https://dandi.centerforopenneuroscience.org . What we...

ATM seems to be required according to https://github.com/datalad/datalad-registry/pull/261 ``` File "/usr/local/lib/python3.9/dist-packages/datalad_metalad/extract.py", line 461, in perform_dataset_metadata_extraction if extractor.get_required_content() is False: File "/usr/local/lib/python3.9/dist-packages/datalad_neuroimaging/extractors/bids_dataset.py", line 150, in get_required_content bids_dir = _find_bids_root(self.dataset.path) File "/usr/local/lib/python3.9/dist-packages/datalad_neuroimaging/extractors/bids_dataset.py",...

ds000174 participants is problematic for pybids

1

just want to file to check in detail later ```shell $> DATALAD_EXC_STR_TBLIMIT=10 datalad --dbg aggregate-metadata --force-extraction --incremental $PWD [INFO ] Aggregate metadata for dataset /mnt/btrfs/datasets/datalad/crawl/openfmri/ds000174 Metadata extraction: 60%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊ | 3.00/5.00...

cfg_bids -- template it out

1

I first wanted to check on resistance or desire for such a change. I wondered to move "templating" of some files (e.g. dataset_description.json, CHANGES, README) from https://github.com/nipy/heudiconv/blob/master/heudiconv/bids.py#L33 into the cfg_bids...

BF: ignore broken derivatives

3

I CPed #72 as well since otherwise couldn't install in a local venv for some reason. Most likely testing would fail probably for the same GitPython 3.x regressions as in...

``` (git-annex)lena:/tmp/mnt/ds000001[master]git-annex $> datalad meta-extract bids [ERROR ] TypeError('PosixPath' object is not subscriptable) (TypeError) (dev3) 1 35958 ->1.....................................:Tue 01 Feb 2022 09:32:42 AM EST:. (git-annex)lena:/tmp/mnt/ds000001[master]git-annex $> datalad --dbg meta-extract bids...

Something to keep in mind: - if not anonymized (e.g. we do not do that in heudiconv yet) dates might leak sensitive information. So we might want to provide ad-hoc...

ATM we have `cfg_bids` which - sets up .gitattributes to have some files directly in git - sets up metadata extraction configuration But besides BIDS I keep running into the...

Become compatible with upcoming pybids 0.9.0

1

see https://github.com/bids-standard/pybids/issues/442 which is probably a main culprit , but there could be more @bpoldrack - can you take over on this?