--datalad option : Can it aggregate-metadata by individual subject/session to be used by datalad metadata search?

[ted-strauss-K1]

I have converted a collection of dicoms to BIDS using heudiconv, with the datalad option, and passing multiple dicoms by subject option -s.

Dicom metadata have been transferred into .heudiconv metadata files, e.g. .heudiconv/DICOM-NAME/info/dicominfo.tsv, I would like to make that available to datalad search. Running datalad aggregate-metadata only seems to capture top-level contents, and ignores lower level BIDS metadata files.

Is there a way to convince datalad to ingest BIDS json and tsv metadata so it will be available to datalad searches?

[yarikoptic]

For DICOMs, you would need to have dicoms around and enable 'dicom' extractor. With current heudiconv approach to DICOMS (storing them in the tarballs), there is no way to "extract" it (see related datalad/datalad-neuroimaging#32). So you would want to either add dicoms manually extracted from those tarballs, or just add another (sub?)dataset with the original dicoms, where you actually extract metadata.

For bids, you need to enable bids extractor (and probably you would want nifti1 as well)
smth like

git config -f .datalad/config --add datalad.metadata.nativetype nifti1;
git config -f .datalad/config --add datalad.metadata.nativetype bids

in the dataset where you want to enable those. Note that you would need datalad-neuroimaging extension installed

[ted-strauss-K1]

Ok I have:

• installed datalad-neuroimaging extension
• re-run heudiconv to convert a dicom to bids
• run the git config statements above in the heudiconv output folder
• then attempted to regenerate metadata, see below:

% datalad aggregate-metadata -d . -r --update-mode all  

[INFO   ] Aggregate metadata for dataset /path/to/file 
[ERROR  ] ("Failed to load metadata extractor for '%s', broken dataset configuration (%s)?: %s", u'bids', <Dataset path=/path/to/file>, "pybids 0.6.4 has no such extra feature 'analysis' [__init__.py:requires:2615]") [metadata.py:_get_metadata:531] (ValueError) 

[yarikoptic]

Let's see if pybids authorities return back analysis or we just drop it ;-)
https://github.com/INCF/pybids/pull/218/files
I guess you could try to pip install pybids==0.5.1 which would match the version which I used and it worked...
that is sad, but I do not see a way in setuptools to declare alternative dependencies, so I guess we will just demand a recent pybids from now on to address it on our end: datalad/datalad-neuroimaging#39 .